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Open AccessArticle

Phylodynamics of Influenza A/H1N1pdm09 in India Reveals Circulation Patterns and Increased Selection for Clade 6b Residues and Other High Mortality Mutants

by Dillon C. Adam 1,*, 1,2,3,† and 1,3,4,†
Biosecurity Program, The Kirby Institute, Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, Australia
Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
College of Health Solutions, Arizona State University, Phoenix, AZ 85004, USA
College of Public Service & Community Solutions, Arizona State University, Tempe, AZ 85004, USA
Author to whom correspondence should be addressed.
Joint Senior Authorship.
Viruses 2019, 11(9), 791;
Received: 26 July 2019 / Revised: 23 August 2019 / Accepted: 24 August 2019 / Published: 27 August 2019
(This article belongs to the Special Issue Emerging Viruses: Surveillance, Prevention, Evolution and Control)
The clinical severity and observed case fatality ratio of influenza A/H1N1pdm09 in India, particularly in 2015 and 2017 far exceeds current global estimates. Reasons for these frequent and severe epidemic waves remain unclear. We used Bayesian phylodynamic methods to uncover possible genetic explanations for this, while also identifying the transmission dynamics of A/H1N1pdm09 between 2009 and 2017 to inform future public health interventions. We reveal a disproportionate selection at haemagglutinin residue positions associated with increased morbidity and mortality in India such as position 222 and clade 6B characteristic residues, relative to equivalent isolates circulating globally. We also identify for the first time, increased selection at position 186 as potentially explaining the severity of recent A/H1N1pdm09 epidemics in India. We reveal national routes of A/H1N1pdm09 transmission, identifying Maharashtra as the most important state for the spread throughout India, while quantifying climactic, ecological, and transport factors as drivers of within-country transmission. Together these results have important implications for future A/H1N1pdm09 surveillance and control within India, but also for epidemic and pandemic risk prediction around the world. View Full-Text
Keywords: Influenza; public health; phylogenetics; India Influenza; public health; phylogenetics; India
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Adam, D.C.; Scotch, M.; MacIntyre, C.R. Phylodynamics of Influenza A/H1N1pdm09 in India Reveals Circulation Patterns and Increased Selection for Clade 6b Residues and Other High Mortality Mutants. Viruses 2019, 11, 791.

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