Cowpox in zoo and wild animals in the United Kingdom.

Cowpox virus is considered to be a re-emerging zoonotic pathogen and a public health threat due to increasing numbers of cases in humans and animals in Europe over the past decade, including within the United Kingdom (UK). We present epidemiological data and diagnostic features of 27 recent, naturally occurring cowpox cases in zoo and wild animals across the UK, including the first reports of cowpox in two snow leopards (Panthera uncia), a Bengal tiger (Panthera tigris tigris), three Chilean pudus (Pudu puda), a Malayan tapir (Tapirus indicus) and a Eurasian otter (Lutra lutra), and the first reports of Orthopoxvirus infection in a lar gibbon (Hylobates lar), a Southern tamandua (Tamandua tetradactyla) and an aardvark (Orycteropus afer). This study provides a detailed overview of cowpox infections in a wide range of non-domestic animal species, presents a range of methods for diagnosis and demonstrates the value of retrospective analysis of pathology surveillance in revealing epidemiological links.

Use of Next Generation Sequencing to study two cowpox virus outbreaks.

BACKGROUND: Between 2008 and 2011 about 40 cases of human cowpox were reported from Germany and France. Infections had been acquired via close contact to infected, young pet rats. An identical and unique sequence of the hemagglutinin gene was found in various cowpox virus (CPXV) isolates pointing to a common source of infection. In a second CPXV outbreak in cats in a small animal clinic in Germany in 2015, four out of five hospitalized cats showed identical hemagglutinin sequences and thus, a hospital-acquired transmission had been assumed. Next-Generation Sequencing was performed in order to re-investigate the outbreaks, as epidemiological data could not confirm all cases. METHODS: Homogenates of lesion material from rats, cats and humans were cultivated in cell culture. The genomes of four virus isolates, nine CPXVs from our strain collections and from DNA of three paraffin-embedded lesion materials were determined by Next Generation Sequencing (NGS). For phylogenetic analyses a MAFFT-alignment was generated. A distance matrix based on concatenated SNPs was calculated and plotted as dendrogram using Unweighted Pair Group Method with Arithmetic mean (UPGMA) for visualization. RESULTS: Aligning of about 200.000 nucleotides of 8 virus isolates associated with the pet rat outbreak revealed complete identity of six genomes, the remainder two genomes differed in as little as 3 SNPs. When comparing this dataset with four already published CPXV genomes also associated with the pet rat outbreak, again a maximum difference of 3 SNPs was found. The outbreak which lasted from 2008 till 2011 was indeed caused by a single strain which has maintained an extremely high level of clonality over 4 years. Aligning genomic sequences from four cases of feline cowpox revealed 3 identical sequences and one sequence which differed in 65 nucleotides. Although identical hemagglutinin sequences had been obtained from four hospitalized cats, genomic sequencing proved that a hospital-acquired transmission had occurred in only three cats. CONCLUSION: Analyzing the rather short sequence of the hemagglutinin gene is not sufficient to conduct molecular trace back analyses. Instead, whole genome sequencing is the method of choice which can even be applied to paraffin-embedded specimens.

Cowpox virus: What's in a Name?

Traditionally, virus taxonomy relied on phenotypic properties; however, a sequence-based virus taxonomy has become essential since the recent requirement of a species to exhibit monophyly. The species Cowpox virus has failed to meet this requirement, necessitating a reexamination of this species. Here, we report the genomic sequences of nine Cowpox viruses and, by combining them with the available data of 37 additional genomes, confirm polyphyly of Cowpox viruses and find statistical support based on genetic data for more than a dozen species. These results are discussed in light of the current International Committee on Taxonomy of Viruses species definition, as well as immediate and future implications for poxvirus taxonomic classification schemes. Data support the recognition of five monophyletic clades of Cowpox viruses as valid species.

Complete Genome Sequence of the Embu Virus Strain SPAn880.

We report the complete genome sequence of the Embu virus. The genome consists of 185,139 bp and is nearly identical to that of the Cotia virus. This is the first report on the Embu virus genome sequence, which has been considered an unclassified poxvirus until now.

Isolation and molecular characterization of a tick-borne encephalitis virus strain from a new tick-borne encephalitis focus with severe cases in Bavaria, Germany.

Tick-borne encephalitis (TBE) is the most important viral infection transmitted by ticks in Central Europe. In Germany, where TBE was classified as a notifiable disease in 2001, a highly variable number of clinically apparent human cases was reported in the last few years, ranging from the lowest number of 238 in 2007 to a maximum of 546 in 2006. The dynamics of the virus and its vector tick remain poorly understood. We investigated a highly active TBE focus in south-eastern Germany where from 2003 to 2008 a total of 9 clinical human cases was diagnosed. Three out of these 9 cases were fatal indicating an unusually high mortality rate possibly due to a highly virulent TBEV strain. From 2005 till 2008, 2150 Ixodes ricinus ticks were collected and tested for the presence of TBE virus. Five TBEV-positive ticks were detected by real-time RT-PCR. A viable virus strain was isolated from one of the positive ticks sampled in 2005. This is the first TBE virus isolate from a tick in Germany for 30 years. Sequencing of the full-length genome of this virus strain (AS33) revealed 2 unique amino acid substitutions in the envelope protein known to play a role in the pathogenicity of TBE virus. Amplification of the envelope gene using 2 TBEV-PCR-positive ticks from 2006 also showed these particular mutations indicating that this TBE virus strain was present in at least 2 consecutive years. The entire sampling area was divided into smaller sectors for the exact location of TBEV-positive ticks. Virus-positive ticks were found to be randomly distributed throughout the investigated focus, which is used as recreational area by the local people.