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

Abstract

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.

Use of Next Generation Sequencing to study two cowpox virus outbreaks

“…The genetic diversity of CPXVs is also reflected by different lengths of the HA ORF, ranging from 816 bp to 963 bp. A recent phylogenetic analysis of 83 full-length OPV genomes [7] confirmed the polyphyletic character of the species CPXV and the existence of at least four different clades had been assumed.…”

“…Typing of and differentiating the species CPXV and VACV is also possible with the restriction that some CPXV strains might be mistyped as VACVs (Figure 1 and Table S1, CPXV groups C001-3, C053 and C063). According to whole genome analysis, these strains form a separate clade referred to as "VACV-like" CPXV [7] which has a common ancestor with the species VACV. According to the species definition of the International Committee on Taxonomy of Viruses the taxonomic classification of CPXVs has to be revisited to avoid confusion.…”

“…With use of Next-Generation-Sequencing, knowledge of genetic epidemiology of orthopoxviruses has increased during the last two to three years [6], [7], [26]. Creating and updating reliable databases of orthopoxvirus genomes would even allow a better understanding of genetic diversity and clonality.…”

“…Sequences marked with an asterisk (*) had been determined in this study. Colored bars indicate three different CPXV-clades according to Franke [7] Pet rat-associated outbreak…”

“…This genetic variation can be explained by the existence of local variants which have evolved over time in a rodent reservoir [2]. Recently, results of phylogenetic analyses of 58 full-length CPXV genomes confirm the polyphyletic character of the species CPXV which consists of at least four different clades and several variants [6], [7].…”