Yi Guan

Summary We present an r package, ggtree , which provides programmable visualization and annotation of phylogenetic trees. ggtree can read more tree file formats than other softwares, including newick , nexus , NHX , phylip and jplace formats, and support visualization of phylo, multiphylo, phylo4, phylo4d, obkdata and phyloseq tree objects defined in other r packages. It can also extract the tree/branch/node‐specific and other data from the analysis outputs of beast , epa , hyphy , paml , phylodog , pplacer , r8s , raxml and revbayes software, and allows using these data to annotate the tree. The package allows colouring and annotation of a tree by numerical/categorical node attributes, manipulating a tree by rotating, collapsing and zooming out clades, highlighting user selected clades or operational taxonomic units and exploration of a large tree by zooming into a selected portion. A two‐dimensional tree can be drawn by scaling the tree width based on an attribute of the nodes. A tree can be annotated with an associated numerical matrix (as a heat map), multiple sequence alignment, subplots or silhouette images. The package ggtree is released under the artistic‐2.0 license . The source code and documents are freely available through bioconductor ( http://www.bioconductor.org/packages/ggtree ).

A novel coronavirus (SCoV) is the etiological agent of severe acute respiratory syndrome (SARS). SCoV-like viruses were isolated from Himalayan palm civets found in a live-animal market in Guangdong, China. Evidence of virus infection was also detected in other animals (including a raccoon dog, Nyctereutes procyonoides) and in humans working at the same market. All the animal isolates retain a 29-nucleotide sequence that is not found in most human isolates. The detection of SCoV-like viruses in small, live wild mammals in a retail market indicates a route of interspecies transmission, although the natural reservoir is not known.

A phylogenetic analysis of swine-origin H1N1 influenza A virus provides evidence that the virus is a reassortment possessing genes from avian, swine and human origin viruses. The pandemic virus appears to have evolved in way typical of swine flu sequences prior to entering humans, and is derived from several viruses circulating in swine. Initial transmission to humans appears to have occurred several months before recognition of the outbreak. An estimate of the gaps in genetic surveillance points to a period of years between the reassortment of swine lineages and the transfer to humans and the multiple genetic ancestry is inconsistent with an artificial origin for the virus. The gaps in out knowledge revealed by this work highlight the need for the systematic surveillance of influence in swine as a means of identifying potentially pandemic strains before they cross into human populations. Evolutionary analysis of swine-origin H1N1 influenza A virus provides evidence that it was derived from several viruses circulating in swine and that it possesses genes from avian, swine and human origin. Furthermore, transmission to humans may have occurred several months before recognition of the current outbreak. In March and early April 2009, a new swine-origin influenza A (H1N1) virus (S-OIV) emerged in Mexico and the United States1. During the first few weeks of surveillance, the virus spread worldwide to 30 countries (as of May 11) by human-to-human transmission, causing the World Health Organization to raise its pandemic alert to level 5 of 6. This virus has the potential to develop into the first influenza pandemic of the twenty-first century. Here we use evolutionary analysis to estimate the timescale of the origins and the early development of the S-OIV epidemic. We show that it was derived from several viruses circulating in swine, and that the initial transmission to humans occurred several months before recognition of the outbreak. A phylogenetic estimate of the gaps in genetic surveillance indicates a long period of unsampled ancestry before the S-OIV outbreak, suggesting that the reassortment of swine lineages may have occurred years before emergence in humans, and that the multiple genetic ancestry of S-OIV is not indicative of an artificial origin. Furthermore, the unsampled history of the epidemic means that the nature and location of the genetically closest swine viruses reveal little about the immediate origin of the epidemic, despite the fact that we included a panel of closely related and previously unpublished swine influenza isolates. Our results highlight the need for systematic surveillance of influenza in swine, and provide evidence that the mixing of new genetic elements in swine can result in the emergence of viruses with pandemic potential in humans2.