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What happened after the initial global spread of pandemic human influenza virus A (H1N1)? A population genetics approach.

ABSTRACT: Viral population evolution dynamics of influenza A is crucial for surveillance and control. In this paper we analyzed viral genetic features during the recent pandemic caused by the new influenza human virus A H1N1, using a conventional population genetics approach based on 4689 hemagglutinin (HA) and neuraminidase (NA) sequences available in GenBank submitted between March and December of 2009. This analysis showed several relevant aspects: a) a scarce initial genetic variability within the viral isolates from some countries that increased along 2009 when influenza was dispersed around the world; b) a worldwide virus polarized behavior identified when comparing paired countries, low differentiation and high gene flow were found in some pairs and high differentiation and moderate or scarce gene flow in others, independently of their geographical closeness, c) lack of positive selection in HA and NA due to increase of the population size of virus variants, d) HA and NA variants spread in a few months all over the world being identified in the same countries in different months along 2009, and e) containment of viral variants in Mexico at the beginning of the outbreak, probably due to the control measures applied by the government.

SUBMITTER: Martinez-Hernandez F

PROVIDER: S-EPMC2936310 | biostudies-literature | 2010 Aug

REPOSITORIES: biostudies-literature

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What happened after the initial global spread of pandemic human influenza virus A (H1N1)? A population genetics approach.

Martinez-Hernandez Fernando F Jimenez-Gonzalez Diego Emiliano DE Martinez-Flores Arony A Villalobos-Castillejos Guiehdani G Vaughan Gilberto G Kawa-Karasik Simon S Flisser Ana A Maravilla Pablo P Romero-Valdovinos Mirza M

Virology journal 20100820

Viral population evolution dynamics of influenza A is crucial for surveillance and control. In this paper we analyzed viral genetic features during the recent pandemic caused by the new influenza human virus A H1N1, using a conventional population genetics approach based on 4689 hemagglutinin (HA) and neuraminidase (NA) sequences available in GenBank submitted between March and December of 2009. This analysis showed several relevant aspects: a) a scarce initial genetic variability within the vir ...[more]

PMID: 20727188

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Project description:BACKGROUND: Confirmed H1N1 cases during late spring and summer 2009 in various countries showed a substantial age shift between importations and local transmission cases, with adults mainly responsible for seeding unaffected regions and children most frequently driving community outbreaks. METHODS: We introduce a multi-host stochastic metapopulation model with two age classes to analytically investigate the role of a heterogeneously mixing population and its associated non-homogeneous travel behaviors on the risk of a major epidemic. We inform the model with demographic data, contact data and travel statistics of Europe and Mexico, and calibrate it to the 2009 H1N1 pandemic early outbreak. We allow for variations of the model parameters to explore the conditions of invasion under different scenarios. RESULTS: We derive the expression for the potential of global invasion of the epidemic that depends on the transmissibility of the pathogen, the transportation network and mobility features, the demographic profile and the mixing pattern. Higher assortativity in the contact pattern greatly increases the probability of spatial containment of the epidemic, this effect being contrasted by an increase in the social activity of adults vs. children. Heterogeneous features of the mobility network characterizing its topology and traffic flows strongly favor the invasion of the pathogen at the spatial level, as also a larger fraction of children traveling. Variations in the demographic profile and mixing habits across countries lead to heterogeneous outbreak situations. Model results are compatible with the H1N1 spatial transmission dynamics observed. CONCLUSIONS: This work illustrates the importance of considering age-dependent mixing profiles and mobility features coupled together to study the conditions for the spatial invasion of an emerging influenza pandemic. Its results allow the immediate assessment of the risk of a major epidemic for a specific scenario upon availability of data, and the evaluation of the potential effectiveness of public health interventions targeting specific age groups, their interactions and mobility behaviors. The approach provides a general modeling framework that can be used for other types of partitions of the host population and applied to different settings.

Dataset Information

What happened after the initial global spread of pandemic human influenza virus A (H1N1)? A population genetics approach.

Publications

What happened after the initial global spread of pandemic human influenza virus A (H1N1)? A population genetics approach.

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