Phylodynamics of H1N1/2009 influenza reveals the transition from host adaptation to immune-driven selection

Su, Yvonne C. F.; Bahl, Justin; Joseph, Udayan; Butt, Ka Man; Peck, Heidi; Koay, Evelyn Siew Chuan; Oon, Lynette; Barr, Ian G.; Vijaykrishna, Dhanasekaran; Smith, Gavin J. D.

doi:10.1038/ncomms8952

Cited by 120 publications

(144 citation statements)

References 67 publications

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“…Since the majority of the NA protein residues of influenza A and B viruses showed ω < 1, it suggests that the amino acids in this protein are under purifying selection. These findings are consistent with previous studies, which reported the overall ω values for the NA genes of 0.30 for seasonal A(H1N1), 0.32 for A(H1N1)pdm09, 0.29 for A(H3N2), and 0.20–0.31 for influenza B virus [3, 51, 54, 57]. The selection pressure of NA of A(H3N2) in German was 0.21, while in Taiwan it was 0.37 [58–59].…”

Section: Discussionsupporting

confidence: 93%

“…The MCC tree from the Bayesian timescale phylogenetic analysis of the NA from seasonal influenza viruses circulating in Thailand is consistent with previous studies and highlights how circulating strains are continually drifting [3, 51, 54] whereby strains which are unable to evade the host immune system are eliminated [64]. The evolutionary patterns of the NA gene indicated a more rapid genetic drift for influenza A than influenza B virus due to higher nucleotide substitution rate, although there was more genetic diversity in influenza B than in influenza A virus.…”

Section: Discussionsupporting

confidence: 86%

“…Since 1977, the seasonal influenza A(H1N1), A(H1N1)pdm09, A(H3N2), and the influenza B virus have co-circulated globally [2–3]. Antivirals against influenza virus are effective for the prevention of these viral infections and have been shown to reduce the duration of infection, the severity of illness, and mortality [4–6].…”

Section: Introductionmentioning

confidence: 99%

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Evolution of the neuraminidase gene of seasonal influenza A and B viruses in Thailand between 2010 and 2015

et al. 2017

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The neuraminidase inhibitors (NAIs) oseltamivir and zanamivir are commonly used for the treatment and control of influenza A and B virus infection. However, the emergence of new influenza virus strains with reduced susceptibility to NAIs may appear with the use of these antivirals or even naturally. We therefore screened the neuraminidase (NA) sequences of seasonal influenza virus A(H1N1), A(H1N1)pdm09, A(H3N2), and influenza B virus strains identified in Thailand for the presence of substitutions previously reported to reduce susceptibility to NAIs. We initially examined oseltamivir resistance (characterized by the H275Y mutation in the NA gene) in 485 A(H1N1)pdm09 strains circulating in Thailand and found that 0.82% (4/485) had this substitution. To further evaluate the evolution of the NA gene, we also randomly selected 98 A(H1N1)pdm09, 158 A(H3N2), and 69 influenza B virus strains for NA gene amplification and sequencing, which revealed various amino acid mutations in the active site of the NA protein previously shown to be associated with reduced susceptibility to NAIs. Phylogenetic analysis of the influenza virus strains from this study and elsewhere around the world, together with the estimations of nucleotide substitution rates and selection pressure, and the predictions of B-cell epitopes and N-linked glycosylation sites all provided evidence for the ongoing evolution of NA. The overall rates of NA evolution for influenza A viruses were higher than for influenza B virus at the nucleotide level, although influenza B virus possessed more genealogical diversity than that of influenza A viruses. The continual surveillance of the antigenic changes associated with the NA protein will not only contribute to the influenza virus database but may also provide a better understanding of selection pressure exerted by antiviral use.

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Section: Discussionsupporting

confidence: 93%

Section: Discussionsupporting

confidence: 86%

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Evolution of the neuraminidase gene of seasonal influenza A and B viruses in Thailand between 2010 and 2015

et al. 2017

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“…153 Several adaptive changes of specific host residues have been reported that contributed to the establishment of this swine virus in humans, observed especially from viruses isolated during the early phase of the pandemic, with the later circulating viruses showing mutations involved in antigenic escape within human hosts. 154 The 2009 pandemic H1N1 (pH1N1) viruses did not contain the Lys-627 or Asn-701 substitutions that were considered indicative of mammalian adaptation, 43,155,156 and it now appears these substitutions are not required for swine to human transmission. Indeed, when the mammalian-like Lys-627 and Asn-701 residues were introduced, a significant increase in polymerase activity and viral pathogenesis was observed, 155,156 but this replicative advantage of the mutation was not necessary for the initial establishment of the avian polymerase in TRS lineage and subsequently human pH1N1 viruses.…”

Section: Pigs: the Mixing Vessel?mentioning

confidence: 99%

The ecology and adaptive evolution of influenza A interspecies transmission

Joseph

Vijaykrishna

et al. 2016

Influenza Resp Viruses

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100

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Since 2013, there have been several alarming influenza‐related events; the spread of highly pathogenic avian influenza H5 viruses into North America, the detection of H10N8 and H5N6 zoonotic infections, the ongoing H7N9 infections in China and the continued zoonosis of H5N1 viruses in parts of Asia and the Middle East. The risk of a new influenza pandemic increases with the repeated interspecies transmission events that facilitate reassortment between animal influenza strains; thus, it is of utmost importance to understand the factors involved that promote or become a barrier to cross‐species transmission of Influenza A viruses (IAVs). Here, we provide an overview of the ecology and evolutionary adaptations of IAVs, with a focus on a review of the molecular factors that enable interspecies transmission of the various virus gene segments.

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“…On the other hand, the collection of the huge amount of data necessary for rigorous large-scale field studies is often impossible due to economical and practical constraints. The development of a theoretical framework and mathematical models to reconstruct evolutionary features and population history of rapidly evolving viruses offers a great opportunity to reconcile and investigate viral epidemiology and evolution [8][9][10][11], an approach that has been proven effective for the study of many human [12][13][14][15][16] and animal [17][18][19][20] diseases.…”

Section: Contents Lists Available At Sciencedirectmentioning

confidence: 99%

Effect of different vaccination strategies on IBV QX population dynamics and clinical outbreaks

Franzo

Tucciarone

Blanco³

et al. 2016

Vaccine

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The extreme variability and rapid evolution of Infectious bronchitis virus (IBV) has always represented the key challenge for its control because of the limited cross-protection among different strains. Several experimental trials have proven a broadening of the protection spectrum when animals are vaccinated with multiple genotypes. Nevertheless, the conditions of vaccine administration in field are so different that the generalization of experimental results is, at least, questionable. In the present study a large scale epidemiological-phylodynamic approach was used to reconstruct the demographic history of the major field genotype (i.e. the QX one) circulating in Italy and Spain. These two countries were selected because, even if they share a comparable epidemiological scenario, the implemented vaccination protocols did not vary in Spain while changed dramatically in Italy over the time period considered. One hundred and ninety-five Italian and 98 Spanish non-recombinant sequences of the hyper-variable region of the S1 gene obtained between 2012 and 2016 were analyzed using a serial coalescent-based approach to reconstruct viral population history over time. While the IBV QX population dynamics remained constant in Spain, a much more complex pattern was evidenced in Italy; both in terms of viral population size and clinical outbreak frequency. Remarkably, a strong association with changes in vaccination strategies was recognized. This allowed demonstrating, by accomplishing all Hill's criteria for causation, the cause-effect relationship between the vaccine administration/withdrawal and the variation in viral population dynamics and, above all, IBV related outbreaks. Thus, a robust confirmation about the efficacy of IBV vaccination in field conditions was provided. Additionally, the history herein reported testifies the primary importance of rigorously planning not only the intervention strategies but also their monitoring and evaluation.

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Phylodynamics of H1N1/2009 influenza reveals the transition from host adaptation to immune-driven selection

Cited by 120 publications

References 67 publications

Evolution of the neuraminidase gene of seasonal influenza A and B viruses in Thailand between 2010 and 2015

Evolution of the neuraminidase gene of seasonal influenza A and B viruses in Thailand between 2010 and 2015

The ecology and adaptive evolution of influenza A interspecies transmission

Effect of different vaccination strategies on IBV QX population dynamics and clinical outbreaks

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