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Viruses 2017, 9(6), 142;

Classification of Cowpox Viruses into Several Distinct Clades and Identification of a Novel Lineage

Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald, Germany
Bundeswehr Institute of Microbiology, Neuherbergstr 11, 80937 Munich, Germany
These authors contributed equally to this work.
Author to whom correspondence should be addressed.
Academic Editor: Eric O. Freed
Received: 22 April 2017 / Revised: 24 May 2017 / Accepted: 5 June 2017 / Published: 10 June 2017
(This article belongs to the Special Issue Smallpox and Emerging Zoonotic Orthopoxviruses: What Is Coming Next?)
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Cowpox virus (CPXV) was considered as uniform species within the genus Orthopoxvirus (OPV). Previous phylogenetic analysis indicated that CPXV is polyphyletic and isolates may cluster into different clades with two of these clades showing genetic similarities to either variola (VARV) or vaccinia viruses (VACV). Further analyses were initiated to assess both the genetic diversity and the evolutionary background of circulating CPXVs. Here we report the full-length sequences of 20 CPXV strains isolated from different animal species and humans in Germany. A phylogenetic analysis of altogether 83 full-length OPV genomes confirmed the polyphyletic character of the species CPXV and suggested at least four different clades. The German isolates from this study mainly clustered into two CPXV-like clades, and VARV- and VACV-like strains were not observed. A single strain, isolated from a cotton-top tamarin, clustered distantly from all other CPXVs and might represent a novel and unique evolutionary lineage. The classification of CPXV strains into clades roughly followed their geographic origin, with the highest clade diversity so far observed for Germany. Furthermore, we found evidence for recombination between OPV clades without significant disruption of the observed clustering. In conclusion, this analysis markedly expands the number of available CPXV full-length sequences and confirms the co-circulation of several CPXV clades in Germany, and provides the first data about a new evolutionary CPXV lineage. View Full-Text
Keywords: cowpox virus; Orthopoxvirus; poxvirus; recombination; phylogeny; genetic diversity; Germany cowpox virus; Orthopoxvirus; poxvirus; recombination; phylogeny; genetic diversity; Germany

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Franke, A.; Pfaff, F.; Jenckel, M.; Hoffmann, B.; Höper, D.; Antwerpen, M.; Meyer, H.; Beer, M.; Hoffmann, D. Classification of Cowpox Viruses into Several Distinct Clades and Identification of a Novel Lineage. Viruses 2017, 9, 142.

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