From where did the 2009 'swine-origin' influenza A virus (H1N1) emerge?

Abstract

The swine-origin influenza A (H1N1) virus that appeared in 2009 and was first found in human beings in Mexico, is a reassortant with at least three parents. Six of the genes are closest in sequence to those of H1N2 'triple-reassortant' influenza viruses isolated from pigs in North America around 1999-2000. Its other two genes are from different Eurasian 'avian-like' viruses of pigs; the NA gene is closest to H1N1 viruses isolated in Europe in 1991-1993, and the MP gene is closest to H3N2 viruses isolated in Asia in 1999-2000. The sequences of these genes do not directly reveal the immediate source of the virus as the closest were from isolates collected more than a decade before the human pandemic started. The three parents of the virus may have been assembled in one place by natural means, such as by migrating birds, however the consistent link with pig viruses suggests that human activity was involved. We discuss a published suggestion that unsampled pig herds, the intercontinental live pig trade, together with porous quarantine barriers, generated the reassortant. We contrast that suggestion with the possibility that laboratory errors involving the sharing of virus isolates and cultured cells, or perhaps vaccine production, may have been involved. Gene sequences from isolates that bridge the time and phylogenetic gap between the new virus and its parents will distinguish between these possibilities, and we suggest where they should be sought. It is important that the source of the new virus be found if we wish to avoid future pandemics rather than just trying to minimize the consequences after they have emerged. Influenza virus is a very significant zoonotic pathogen. Public confidence in influenza research, and the agribusinesses that are based on influenza's many hosts, has been eroded by several recent events involving the virus. Measures that might restore confidence include establishing a unified international administrative framework coordinating surveillance, research and commercial work with this virus, and maintaining a registry of all influenza isolates.

Reassortment Events among Swine Influenza A Viruses in China: Implications for the Origin of the 2009 Influenza Pandemic

“…It is generally accepted that all these parents belong to either the TR H1N2 swine influenza virus lineage originally present in pigs in North America or the EA H1N1 swine virus lineage circulating in pigs in European countries (6,7,19). However, cocirculation of both parent virus lineages in pigs, which could facilitate the reassortment events leading to the genesis and emergence of this TR-EA pandemic virus, is only known, from accessible epidemiological data, to have occurred in China since 2001.…”

Pig producers’ perceptions of the Influenza Pandemic H1N1/09 outbreak and its effect on their biosecurity practices in Australia

“…By July 2010, the H1N1/09 virus had caused more than 18,000 deaths (WHO, 2000b). The H1N1/09 virus is a reassortant with at least three parents, containing genes from swine, avian and human influenza viruses (Gibbs et al, 2009;Kou et al, 2009), which originated in humans. Although no link between an animal and the first human cases has been established (Vallat, 2009), the disease was named 'swine influenza' or 'swine flu' from the start of the outbreak.…”

Avian-Like A (H1N1) Swine Influenza Virus Antibodies among Swine Farm Residents and Pigs in Southern China

“…At present, three main subtypes of the influenza virus are prevalent among pig populations worldwide: H3N2, H1N1, and H1N2 (1). The antigenic and genetic diversity of swine H1N1 viruses have been documented in different regions of the world.…”