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

Fernando Martinez-Hernandez,Pablo Maravilla,Ana Flisser,Guiehdani Villalobos-Castillejos,Mirza Romero-Valdovinos,Simon Kawa-Karasik,Diego Emiliano Jimenez-Gonzalez,Arony Martinez-Flores,Gilberto Vaughan

doi:10.1186/1743-422x-7-196

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.

Highlights

Viral population evolution dynamics of influenza A is crucial for surveillance and control
The previously described genetic diversity analyses were performed with A H1N1 Influenza Database [13] with sequences submitted between April and December 2009, including three or more sequences per country of 500 continuous base pairs, recorded during the initial four months of the pandemics and, for the global analysis, those having at least 750 continuous bp were used
Genetic population indexes were compared in the countries with most sequences reported (USA, Spain, Japan, Mexico and China)

Summary

Introduction

Viral population evolution dynamics of influenza A is crucial for surveillance and control. The previously described genetic diversity analyses were performed with A H1N1 Influenza Database [13] with sequences submitted between April and December 2009 (collection dates and sequence origin are found in addition file 1), including three or more sequences per country of 500 continuous base pairs (bp), recorded during the initial four months of the pandemics and, for the global analysis, those having at least 750 continuous bp were used.

Objectives

Results

Conclusion