The genomic and epidemiological dynamics of human influenza A virus

Rambaut, Andrew; Pybus, Oliver G.; Nelson, Martha I.; Viboud, Cécile; Taubenberger, Jeffery K.; Holmes, Edward C.

doi:10.1038/nature06945

Cited by 857 publications

(1,012 citation statements)

References 46 publications

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“…Presently, tropical and subtropical Asia contribute disproportionately to the evolution of H3N2 [33,34,[50][51][52], which may be due to higher regional transmission [40]. High vaccine coverage in seasonal populations may compound the propensity for Asia to produce antigenically advanced strains that contribute to influenza's long-term evolution.…”

Section: Discussionmentioning

confidence: 99%

The beneficial effects of vaccination on the evolution of seasonal influenza

Wen

Malani

Cobey

2017

Preprint

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Although vaccines against seasonal influenza are designed to protect against currently circulating strains, they may also affect the emergence of antigenically divergent strains and thereby change the rate of antigenic evolution. Such evolutionary effects could change the benefits that vaccines confer to vaccinated individuals and the host population (i.e. private and social benefits). To investigate vaccinations potential evolutionary impacts, we simulated the dynamics of an influenza-like pathogen in an annually vaccinated host population. On average, vaccination decreased the cumulative amount of antigenic evolution of the viral population and the incidence of disease. Vaccination at a 5% random annual vaccination rate (48% cumulative vaccine coverage after 20 years) decreased cumulative evolution by 56% and incidence by 76%. To understand how the evolutionary effects of vaccination might affect its private and social benefits over multiple seasons, we fit linear panel models to simulated infection and vaccination histories. Including the evolutionary effects of vaccination lowered the private benefits by 14% but increased the social benefits by 30% (at a 5% annual vaccination rate) compared to when evolutionary effects were ignored. Thus, in the long term, vaccines' private benefits may be lower and social benefits may be greater than predicted by current measurements of vaccine impact, which do not capture long-term evolutionary effects. These results suggest that conventional vaccines against seasonal influenza could greatly reduce the burden of disease by slowing antigenic evolution like universal vaccines. Furthermore, vaccination's evolutionary effects compound a collective action problem, highlighting the importance on social policies concerning vaccination.

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Section: Discussionmentioning

confidence: 99%

The beneficial effects of vaccination on the evolution of seasonal influenza

Wen

Malani

Cobey

2017

Preprint

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“…In addition, the genetic diversity found within the different sublineages of HMPV was of a very recent origin, and HMPV as a whole was characterized by low levels of standing genetic variation (as reflected in estimates of N e t). Such limited genetic diversity, which is also characteristic of human influenza A virus (Rambaut et al, 2008), as well as other paramyxoviruses (Pomeroy et al, 2008) is most likely due to repeated (annual) population bottlenecks, which periodically purge genetic variation.…”

Section: Discussionmentioning

confidence: 99%

Evolutionary dynamics of human and avian metapneumoviruses

Graaf

Osterhaus

Fouchier

et al. 2008

Journal of General Virology

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Human (HMPV) and avian (AMPV) metapneumoviruses are closely related viruses that cause respiratory tract illnesses in humans and birds, respectively. Although HMPV was first discovered in 2001, retrospective studies have shown that HMPV has been circulating in humans for at least 50 years. AMPV was first isolated in the 1970s, and can be classified into four subgroups, A-D. AMPV subgroup C is more closely related to HMPV than to any other AMPV subgroup, suggesting that HMPV has emerged from AMPV-C upon zoonosis. Presently, at least four genetic lineages of HMPV circulate in human populations -A1, A2, B1 and B2 -of which lineages A and B are antigenically distinct. We used a Bayesian Markov Chain Monte Carlo (MCMC) framework to determine the evolutionary and epidemiological dynamics of HMPV and AMPV-C. The rates of nucleotide substitution, relative genetic diversity and time to the most recent common ancestor (TMRCA) were estimated using large sets of sequences of the nucleoprotein, the fusion protein and attachment protein genes. The sampled genetic diversity of HMPV was found to have arisen within the past 119-133 years, with consistent results across all three genes, while the TMRCA for HMPV and AMPV-C was estimated to have existed around 200 years ago. The relative genetic diversity observed in the four HMPV lineages was low, most likely reflecting continual population bottlenecks, with only limited evidence for positive selection. INTRODUCTIONHuman metapneumovirus (HMPV) is a respiratory pathogen that was first described in 2001 (van den Hoogen et al., 2001). HMPV causes respiratory illnesses ranging from mild upper respiratory symptoms to severe lower respiratory tract disease (van den Hoogen et al., 2001(van den Hoogen et al., , 2003Williams et al., 2004). HMPV is an enveloped, non-segmented, negative-strand RNA virus and was classified as a member of the family Paramyxoviridae, the subfamily Pneumovirinae, the genus Metapneumovirus. HPMV seroprevalence in the human population reaches 100 % by the age of five (van den Hoogen et al., 2001). Experimental HMPV infections in macaques have been shown to induce transient protection , which is in agreement with relatively frequent occurrences of reinfection in humans (Ebihara et al., 2004). HMPV can be divided in two main genetic lineages (A and B), each consisting of at least two sublineages -A1, A2, B1 and B2 (van den Hoogen et al., 2004). Annual circulation of all four lineages has been observed worldwide, with reports of a predominating strain changing on a yearly basis in some studies, but not in others (Galiano et al., 2006;Sloots et al., 2006;van den Hoogen et al., 2004).The only other member of the genus Metapneumovirus is avian metapneumovirus (AMPV). AMPV has been found to infect domestic poultry worldwide, causing acute respiratory infections (Cook, 2000b). AMPVs have been classified into four subgroups, A through to D (BayonAuboyer et al., 1999;Eterradossi et al., 1995;Juhasz & Easton, 1994;Seal, 1998). AMPV subgroups A and B were first detected in...

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“…Widespread influenza outbreaks caused by antigenic drift variants are usually thought to be characterized by reduced genetic diversity of the viruses, either genome-wide or in the hemagglutinin (HA) segment (21)(22)(23). Thus, a widespread outbreak can be reasonably inferred by high sequence similarity of viruses isolated during a specified time span across a broad region.…”

Section: Significancementioning

confidence: 99%

Evolution of the H9N2 influenza genotype that facilitated the genesis of the novel H7N9 virus

Wang

Yin

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

315

340

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The emergence of human infection with a novel H7N9 influenza virus in China raises a pandemic concern. Chicken H9N2 viruses provided all six of the novel reassortant’s internal genes. However, it is not fully understood how the prevalence and evolution of these H9N2 chicken viruses facilitated the genesis of the novel H7N9 viruses. Here we show that over more than 10 y of cocirculation of multiple H9N2 genotypes, a genotype (G57) emerged that had changed antigenicity and improved adaptability in chickens. It became predominant in vaccinated farm chickens in China, caused widespread outbreaks in 2010–2013 before the H7N9 viruses emerged in humans, and finally provided all of their internal genes to the novel H7N9 viruses. The prevalence and variation of H9N2 influenza virus in farmed poultry could provide an important early warning of the emergence of novel reassortants with pandemic potential.

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The genomic and epidemiological dynamics of human influenza A virus

Cited by 857 publications

References 46 publications

The beneficial effects of vaccination on the evolution of seasonal influenza

The beneficial effects of vaccination on the evolution of seasonal influenza

Evolutionary dynamics of human and avian metapneumoviruses

Evolution of the H9N2 influenza genotype that facilitated the genesis of the novel H7N9 virus

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