Molecular epidemiology of influenza A(H1N1)pdm09 virus among humans and swine, Sri Lanka

Abstract

After multiple discrete introductions of influenza A(H1N1)pdm09 virus into Sri Lanka, the virus was transmitted among humans, then swine. The spread of virus between geographically distant swine farms is consistent with virus dispersal associated with a vehicle used for swine transportation, although this remains unproven.

Figure 1

Phylogenetic relationships of influenza A H1N1pdm viruses isolated from human and swine during 2009�?"2012 in Sri Lanka. (A) Maximum likelihood tree generated from a concatenated dataset of 8 gene segment sequences from 1,057 human and 82 swine H1N1pdm viruses isolated globally during 2009�?"2012, and 35 human and 26 swine H1N1pdm viruses isolated in Sri Lanka in 2009�?"2012. Red and green branches represent human (hu) and swine (sw) viruses isolated in Sri Lanka, respectively; gray and blue branches represent globally sampled human and swine viruses, respectively. Highlighted regions (gray) are shown with virus names in (B) and (C), respectively. Support values estimated from 500 maximum likelihood bootstrap replicates are shown along the node for each swine and human clusters identified in Sri Lanka in (A) and for each node with >70% support for (B) and (C).

Figure 2

Phylogeny and divergence times of the concatenated whole genome of 2 swine pandemic influenza A(H1N1) (H1N1pdm) virus clusters (sw 1 and 2) detected in Sri Lanka (A,B) and distribution of swine farms yielding H1N1pdm virus isolates during 2009�?"2013. Gray branches represent global H1N1pdm viruses and black branches represent human and swine H1N1pdm viruses isolated in this study (A, B). Farm of origin is provided for all swine isolates. Gray bars on the tree nodes represent 95% highest posterior density intervals of divergence times. The maximum clade credible tree is summarized from 2 runs of 20 million generations (after the removal of the first 10% as burnin), using the uncorrelated lognormal relaxed clock model, the SRD06 codon based nucleotide substitution model and an exponential coalescent population size, in BEAST ( 7 ). The number of swine H1N1pdm viruses isolated in the farm is provided in brackets (C). The farms from which H1N1pdm viruses were isolated in 2011 are farms A, C, and G. The common transportation truck is the property of the farm M owner. Approximate locations are given.