Temporally structured metapopulation dynamics and persistence of influenza A H3N2 virus in humans

[tetano]

Published online before print November 14, 2011, doi: 10.1073/pnas.1109314108 PNAS November 14, 2011


Temporally structured metapopulation dynamics and persistence of influenza A H3N2 virus in humans

Justin Bahla,b,1,
Martha I. Nelsonc,
Kwok H. Chana,
Rubing Chend,
Dhanasekaran Vijaykrishnaa,b,
Rebecca A. Halpine,
Timothy B. Stockwelle,
Xudong Line,
David E. Wentworthe,
Elodie Ghedine,f,
Yi Guana,
J. S. Malik Peirisa,g,
Steven Rileyh,i,
Andrew Rambautc,j,
Edward C. Holmesc,k, and
Gavin J. D. Smitha,b,1

+ Author Affiliations

aDepartment of Microbiology, State Key Laboratory of Emerging Infectious Diseases,
hDepartment of Community Medicine and School of Public Health, Li Ka Shing Faculty of Medicine, and
gHong Kong University-Pasteur Research Centre, University of Hong Kong, Pokfulam, Hong Kong Special Admnistrative Region, China;
bLaboratory of Virus Evolution, Program in Emerging Infectious Diseases, Duke?National University of Singapore Graduate Medical School, Republic of Singapore 169857;
cFogarty International Center, National Institutes of Health, Bethesda, MD 20892;
dUniversity of Texas Medical Branch, Galveston, TX 77555;
eJ. Craig Venter Institute, Rockville, MD 20850;
fCenter for Vaccine Research, Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261;
iMedical Research Council Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College, London W2 1PG, United Kingdom;
jInstitute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom; and
kCenter for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA 16802

Edited by Peter Palese, Mount Sinai School of Medicine, New York, NY, and approved October 12, 2011 (received for review June 9, 2011)

Abstract

Populations of seasonal influenza virus experience strong annual bottlenecks that pose a considerable extinction risk. It has been suggested that an influenza source population located in tropical Southeast or East Asia seeds annual temperate epidemics. Here we investigate the seasonal dynamics and migration patterns of influenza A H3N2 virus by analysis of virus samples obtained from 2003 to 2006 from Australia, Europe, Japan, New York, New Zealand, Southeast Asia, and newly sequenced viruses from Hong Kong. In contrast to annual temperate epidemics, relatively low levels of relative genetic diversity and no seasonal fluctuations characterized virus populations in tropical Southeast Asia and Hong Kong. Bayesian phylogeographic analysis using discrete temporal and spatial characters reveal high rates of viral migration between urban centers tested. Although the virus population that migrated between Southeast Asia and Hong Kong persisted through time, this was dependent on virus input from temperate regions and these tropical regions did not maintain a source for annual H3N2 influenza epidemics. We further show that multiple lineages may seed annual influenza epidemics, and that each region may function as a potential source population. We therefore propose that the global persistence of H3N2 influenza A virus is the result of a migrating metapopulation in which multiple different localities may seed seasonal epidemics in temperate regions in a given year. Such complex global migration dynamics may confound control efforts and contribute to the emergence and spread of antigenic variants and drug-resistant viruses.


full article

http://www.pnas.org/content/early/2011/11/08/1109314108.abstract

[tetano]

Re: Temporally structured metapopulation dynamics and persistence of influenza A H3N2 virus in humans

Tropical areas aren't the only source of seasonal flu epidemics: study

A commonly held theory says that flu virus originates every year in Southeast and Eastern Asia, making this region the source of seasonal flu epidemics in other parts of the world.

However, researchers at Duke-NUS Graduate Medical School in Singapore have found that influenza virus in tropical areas isn't the only global source of flu epidemics. The international team of scientists involved in the work found that any one of the urban centers they studied could act as a source for a flu epidemic in any other locality.

"We found that these regions are just one node in a network of urban centers connected by air travel, through which flu virus circulates and causes a series of local epidemics that overlap in time," said Gavin Smith, PhD, senior author and Associate Professor in the Program in Emerging Infectious Diseases at Duke-NUS.

The study was published the week of Nov. 14 in the online Early Edition of the Proceedings of the National Academy of Sciences.

The research team chose to study influenza A because it is much more prevalent than both influenza B and C. Influenza is a significant cause of human illness and death worldwide ? the World Health Organization estimates that 250,000 to 500,000 influenza A related deaths occur per year worldwide, and about 49,000 deaths occur in the United States.

..

http://medicalxpress.com/news/2011-11-tropical-areas-arent-source-seasonal.html

[gsgs]

Re: Temporally structured metapopulation dynamics and persistence of influenza A H3N2 virus in humans

http://www.pnas.org/content/early/2011/11/08/1109314108.full.pdf+html

OK, I read the paper (6 pages), but didn't go into all the details, e.g. I don't yet understand what they did in Fig.2B.

I mainly disagree with their conclusions and propositions.

They do appreciate that USA,Europe,NZ,AUS ("temperate") are different from HK,SE-Asia in that they
have seasonal outbreaks in winter with almost no flu in summer.
However strains in temperate regions rarely go back to Asia or re-emerge in the next season.
And the earliest seen variants of new strains are usually from tropical Asia in ~May-Sept. the
preceding year. So temperate regions , i.e. well examined USA are clearly a sink of flu-evolution.

I'm not sure, how it is in HK or SE-Asia, whether their strains fail to survive as well.
If yes, then that doesn't already mean that there is no source-region as they propose.
The source region could be elsewhere (outside their 7 examined regions), my favourite is India.
We have clear evidence that 2-4 successful strains recently were first seen in India