This unexpected finding demonstrates the role of diffuse international networks in the global spread of HIV-1 infection, and the utility of globally sampled viral sequence data in revealing these networks.
The upcoming hyperspectral satellite mission Environmental Mapping and Analysis Program (EnMAP) will provide timely and globally sampled imaging spectrometer data on a frequent basis.
These 54 sequences were aligned with a set of 1,289 globally sampled reference sequences, plus 84 additional sequences from the UK.
In addition, this analysis further demonstrates the utility of globally sampled viral sequence data in unraveling the complex routes by which sexually transmitted infections spread across international borders.
A globally sampled reference sequence set comprising 1,289 previously published subtype C pol gene sequences annotated by country of sampling was obtained from the Los Alamos HIV Sequence Database (www.hiv.lanl.gov).hiv.lanl.gov
Maximum likelihood and Bayesian approaches were used to explore the phylogenetic relationships between 54 sequences identified in this screen, and a set of globally sampled subtype C reference sequences.
For this purpose, we partition globally sampled sequences based on their country of collection.
Globally, samples in both regions were almost perfectly clustered by age group, reflecting distinct patterns of gene expression at each age.
In addition, we identified 319 population-specific miRNA alleles (PSMAs), defined as variants present exclusively in 1 of the 14 globally sampled populations.
Tee et al. (2010) applied globally sampled VP1 sequences and identified three putative sites under positive selection [ 39], suggesting that a more comprehensive sampling may be necessary to identify site under selection.
