Gene families are growing rapidly, but standard methods for inferring phylogenies do not scale to alignments with over 10,000 sequences. We present FastTree, a method for constructing large phylogenies and for estimating their reliability. Instead of storing a distance matrix, FastTree stores sequence profiles of internal nodes in the tree. FastTree uses these profiles to implement neighbor-joining and uses heuristics to quickly identify candidate joins. FastTree then uses nearest-neighbor interchanges to reduce the length of the tree. For an alignment with N sequences, L sites, and a different characters, a distance matrix requires O(N^2) space and O(N^2 L) time, but FastTree requires just O( NLa + N sqrt(N) ) memory and O( N sqrt(N) log(N) L a ) time. To estimate the tree's reliability, FastTree uses local bootstrapping, which gives another 100-fold speedup over a distance matrix. For example, FastTree computed a tree and support values for 158,022 distinct 16S ribosomal RNAs in 17 hours and 2.4 gigabytes of memory. Just computing pairwise Jukes-Cantor distances and storing them, without inferring a tree or bootstrapping, would require 17 hours and 50 gigabytes of memory. In simulations, FastTree was slightly more accurate than neighbor joining, BIONJ, or FastME; on genuine alignments, FastTree's topologies had higher likelihoods. FastTree is available at http://microbesonline.org/fasttree.

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Fast Tree: Computing Large Minimum-Evolution Trees with Profiles instead of a Distance Matrix

VERY few veterinary surgeons have thought fit to write a book on diseases of poultry. Mr. Ernest Gray has done justice to the subject and is to be congratulated on his effort. A book of this size, written by one with specialized knowledge, will add to the value of any library or private bookshelf. Diseases of Poultry Their Aetiology, Diagnosis, Treatment and Control; with a Section on the Normal Anatomy and Physiology of the Fowl. By Ernest Gray. (Lockwood's Agricultural and Horticultural Handbooks.) Pp. x + 198 + 16 plates. (London: Crosby Lockwood and Son, Ltd., 1940.) 9s. 6d. net.

Diseases of Poultry

Viral diseases of farm animals, rather than being a diminishing problem across the world, are now appearing with regularity in areas where they have never been seen before. Across the developing world, viral pathogens such as peste des petits ruminants virus (PPRV) place a huge disease burden on agriculture, in particular affecting small ruminant production and in turn increasing poverty in some of the poorest parts of the world. PPRV is currently considered as one of the main animal transboundary diseases that constitutes a threat to livestock production in many developing countries, particularly in western Africa and south Asia. Infection of small ruminants with PPRV causes a devastating plague and as well as being endemic across much of the developing world, in recent years outbreaks of PPRV have occurred in the European part of Turkey. Indeed, the relevance of many once considered 'exotic' viruses is now also high across the European Union and may threaten further regions across the globe in the future. Here, we review the spread of PPRV across Africa, Asia and into Europe through submissions made to the OIE Regional Reference Laboratories. Further, we discuss current control methods and the development of further tools to aid both diagnosis of the disease and prevention.

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Global distribution of peste des petits ruminants virus and prospects for improved diagnosis and control

Newcastle disease: Evolution of genotypes and the related diagnostic challenges

Over the last three decades, virus-like particles (VLPs) have evolved to become a widely accepted technology, especially in the field of vaccinology. In fact, some VLP-based vaccines are currently used as commercial medical products, and other VLP-based products are at different stages of clinical study. Several remarkable advantages have been achieved in the development of VLPs as gene therapy tools and new nanomaterials. The analysis of published data reveals that at least 110 VLPs have been constructed from viruses belonging to 35 different families. This review therefore discusses the main principles in the cloning of viral structural genes, the relevant host systems and the purification procedures that have been developed. In addition, the methods that are used to characterize the structural integrity, stability, and components, including the encapsidated nucleic acids, of newly synthesized VLPs are analyzed. Moreover, some of the modifications that are required to construct VLP-based carriers of viral origin with defined properties are discussed, and examples are provided.

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Construction and Characterization of Virus-Like Particles: A Review

On August 3, 2018, an outbreak of African swine fever in pigs was reported in China. We subjected a virus from an African swine fever-positive pig sample to phylogenetic analysis. This analysis showed that the causative strain belonged to the p72 genotype II and CD2v serogroup 8.

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Molecular Characterization of African Swine Fever Virus, China, 2018.

Serologic and molecular evidence indicates that peste des petits ruminants virus (PPRV) infection has emerged in goats and sheep in the Ngari region of southwestern Tibet, People’s Republic of China. Phylogenetic analysis confirms that the PPRV strain from Tibet is classified as lineage 4 and is closely related to viruses currently circulating in neighboring countries of southern Asia.

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Zhiliang Wang

Papers

Molecular Characterization of African Swine Fever Virus, China, 2018.

Peste des petits ruminants virus in Tibet, China.

Use of baculovirus expression system for generation of virus-like particles: successes and challenges.

Molecular epidemiological analysis of Newcastle disease virus isolated in China in 2005

Development of one-step real-time RT-PCR assay for detection and quantitation of peste des petits ruminants virus.