Migration and Persistence of Human Influenza A Viruses, Vietnam, 2001–2008

Mai Quynh Le, Ha Minh Lam, Vuong Duc Cuong, Tommy Tsan-Yuk Lam, Rebecca A Halpin, David E Wentworth, Nguyen Tran Hien, Le Thi Thanh, Hoang Vu Mai Phuong, Peter Horby, and Maciej F. Boni

Author affiliations: National Institute for Hygiene and Epidemiology, Hanoi, Vietnam (M.Q. Le, V.D. Cuong, N.T. Hien, L.T. Thanh, H.V.M. Phuong); Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam (H.M. Lam, M.F. Boni); University of Edinburgh, Edinburgh, Scotland, UK (H.M. Lam); University of Oxford, Oxford, UK (T.T.-Y. Lam, P. Horby, M.F. Boni); The J. Craig Venter Institute, Rockville, Maryland, USA (R.A. Halpin, D. E. Wentworth); Oxford University Clinical Research Unit, Hanoi (P. Horby)

Abstract

Understanding global influenza migration and persistence is crucial for vaccine strain selection. Using 240 new human influenza A virus whole genomes collected in Vietnam during 2001–2008, we looked for persistence patterns and migratory connections between Vietnam and other countries. We found that viruses in Vietnam migrate to and from China, Hong Kong, Taiwan, Cambodia, Japan, South Korea, and the United States. We attempted to reduce geographic bias by generating phylogenies subsampled at the year and country levels. However, migration events in these phylogenies were still driven by the presence or absence of sequence data, indicating that an epidemiologic study design that controls for prevalence is required for robust migration analysis. With whole-genome data, most migration events are not detectable from the phylogeny of the hemagglutinin segment alone, although general migratory relationships between Vietnam and other countries are visible in the hemagglutinin phylogeny. It is possible that virus lineages in Vietnam persisted for >1 year.

Understanding influenza dynamics in tropical regions is crucial for understanding global influenza epidemiology because dynamics between temperate and tropical regions are closely linked. Phylogenetic studies have supported eastern Asia, Southeast Asia, and the tropics as potential ecological sources of global influenza circulation (1,2), but others have suggested a variety of geographic regions as potential sources (3–5). Consequently, the role played by the tropics in the global epidemiology of influenza is still uncertain. Viral gene sequence data from tropical countries are crucial for understanding virus migratory routes within the tropics and between tropical and temperate countries.