Complete genomic sequencing of canine distemper virus with nanopore technology during an epizootic event

Canine distemper virus (CDV) endangers a wide range of wild animal populations, can cross species barriers and therefore representing a significant conservational and animal health risk around the globe. During spring to autumn 2021, according to our current estimates a minimum of 50 red foxes (Vulpes vulpes) died of CDV in Hungary, with CDV lesions. Oral, nasal and rectal swab samples were RT-PCR screened for Canine Distemper Virus from red fox carcasses. To investigate in more detail the origins of these CDV strains, 19 complete genomes were sequenced with a pan-genotype CDV-specific amplicon-based sequencing method developed by our laboratory and optimized for the Oxford Nanopore Technologies platform. Phylogenetic analysis of the complete genomic sequences and separately the hemagglutinin gene sequences revealed the role of the Europe lineage of CDV as a causative agent for the current epizootic. Here we highlight the growing importance of fast developing rapid sequencing technologies to aid rapid response activities during epidemics or epizootic events. We also emphasize the urgent need for improved surveillance of CDV, considering the epizootic capability of enzootic strains as reported in the current study. For such future efforts, we provide a novel NGS protocol to facilitate future genomic surveillance studies

Understanding virus and microbial evolution in wildlife through meta-transcriptomics

Wildlife harbors a substantial and largely undocumented diversity of RNA viruses and microbial life forms. RNA viruses and microbes are also arguably the most diverse and dynamic entities on Earth. Despite their evident importance, there are major limitations in our knowledge of the diversity, ecology, and evolution of RNA viruses and microbial communities. These gaps stem from a variety of factors, including biased sampling and the difficulty in accurately identifying highly divergent sequences through sequence similarity-based analyses alone. The implementation of meta-transcriptomic sequencing has greatly contributed to narrowing this gap. In particular, the rapid increase in the number of newly described RNA viruses over the last decade provides a glimpse of the remarkable diversity within the RNA virosphere. The central goal in this thesis was to determine the diversity of RNA viruses associated with wildlife, particularly in an Australian context. To this end I exploited cutting-edge meta-transcriptomic and bioinformatic approaches to reveal the RNA virus diversity within diverse animal taxa, tissues, and environments, with a special focus on the highly divergent "dark matter" of the virome that has largely been refractory to sequence analysis. Similarly, I used these approaches to detect targeted common microbes circulating in vertebrate and invertebrate fauna. Another important goal was to assess the diversity of RNA viruses and microbes as a cornerstone within a new eco-evolutionary framework. By doing so, this thesis encompasses multiple disciplines including virus discovery, viral host-range distributions, microbial-virus and host–parasite interactions, phylogenetic analysis, and pathogen surveillance. In sum, the research presented in this thesis expands the known RNA virosphere as well as the detection and surveillance of targeted microbes in wildlife, providing new insights into the diversity, evolution, and ecology of these agents in nature

Veterinary Microbiology & Parasitology

Numerous pathogens affect animal health and wellbeing and production efficiency. These pathogens also have a considerable impact on social economics, food safety and security, and human health. Infectious diseases that originate from both domesticated animals and wildlife represent one of the greatest threats to human health. Recent studies show that domesticated species harbor approximately 84 times more zoonotic viruses than wild species. Eight of the top 10 mammalian species with the highest number of zoonotic viruses are domestic, such as pigs, cattle, and horses. Many animal parasites are also zoonotic, constituting an additional burden on human health. Furthermore, the rapid emergence and spread of drug-resistant pathogen strains pose new threats to animal and human health. Climate changes will undoubtedly alter the interactions between animals and between animals and humans, which will have a huge impact on the transmission rate of existing pathogens and the emergence of new pathogens or the reemergence of old pathogens. In this special collection, interactions of all major pathogen types, including viruses, bacteria, mites and flies, protozoans, and helminths, and their hosts, such as wild and companion animals and livestock species, are discussed. Further, anthelmintic activities of natural products are evaluated. The relevance and utility of cutting-edge tools, such as immunology, genomics and genetics, microbiome studies and metabolomics, and molecular epidemiology, in dissecting host-pathogen interactions are also discussed. This special collection provides a broad knowledge base that encourages dialogue across a wide distribution of the research community in veterinary microbiology and parasitology

Advances in Parvovirus Research 2020

Viruses of the Parvoviridae family constitute a most diverse and intriguing field of research. Parvoviruses can differ widely in their structure, genome organization and expression, virus–cell interactions, and impact on hosts. The translational implication of research on parvoviruses is relevant, since many viruses are important human and veterinary pathogens, while other viruses can be engineered as tools for oncolytic therapy or as sophisticated gene delivery vectors. Exploring the diversity and inherent complexity in the biology of these apparently simple viruses is a still challenging topic for the scientific community. The Special Issue of Viruses is a collection of recent contributions in the field of parvovirus research, encompassing many aspects of basic and translational research on viruses of the family Parvoviridae, including on their structure, replication, and gene expression in addition to virus–host interactions and the development of vaccines and viral vectors

Zoonoses and Wildlife: One Health Approach

Throughout history, wildlife has been an important source of infectious diseases transmissible to humans. Today, zoonoses with a wildlife reservoir constitute a major public health problem, affecting all continents. The importance of such zoonoses is increasingly recognized, and the need for more attention in this area is being addressed. The total number of zoonoses is unknown, some 1,415 known human pathogens have been catalogued, and 62% are of zoonotic origin [1]. With time, more and more human pathogens are found to be of animal origin. Moreover, most emerging infectious diseases in humans are zoonoses. Wild animals seem to be involved in the epidemiology of most zoonoses and serve as major reservoirs for transmission of zoonotic agents to domestic animals and humans [2]. The concept of the ‘One Health’ approach involving collaboration between veterinary and medical scientists, policy makers, and public health officials, is necessary to foster joint cooperation and control of emerging zoonotic diseases [3]. Zoonotic diseases caused by a wide range of arthropods, bacteria, helminths, protozoans, and viruses can cause serious and even life-threatening clinical conditions in animals, with a number of them also affecting the human population due to their zoonotic potential. The aim of the current Special Issue is to cover recent and novel research trends in zoonotic diseases in wildlife, including the relevant topics related to wildlife, zoonosis, public health, emerging diseases, infectious diseases and parasitic diseases