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

Abstract

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.

Retrospective Detection and Complete Genomic Sequencing of Canine morbillivirus in Eurasian Otter (Lutra lutra) Using Nanopore Technology

“…This will greatly facilitate a better understanding of both the evolution of CDV and epizootic patterns in the near future [ 47 , 64 , 65 , 66 , 67 ]. In our study, we used a recently published pan-genotype CDV-specific amplicon-based sequencing method developed for the Oxford Nanopore Technologies platform [ 51 ]. A key advantage regarding this method is its ability to sequence the entire genome of CDV quickly and efficiently with multiplexed amplicons, without the necessity for in vitro isolation procedures.…”

“…In the last two decades, European, Arctic-like, and European wildlife lineage were detected among dogs. In addition to dogs, CDV infection was detected in wild carnivores, such as the fox ( Vulpes vulpes ), raccoon ( Procyon lotor ), and ferret ( Mustela putorius furo ) [ 51 , 68 , 69 , 70 ].…”

“…Recently, the European lineage of CDV was detected in Germany among raccoons ( Procyon lotor ) from 2015, in red foxes from 2016 [ 74 ], and in Northern Italy in red foxes, badgers, and stone martens between 2018 and 2019 [ 75 ]. In addition to these studies, numerous red foxes were detected in Hungary in 2021, in association with a possible countrywide epizootic event [ 51 ]. Apparently, CDV is a widespread and, at the same time, fairly investigated pathogen among wild carnivores throughout Europe.…”

“…The complete genome sequencing was performed with MinION nanopore sequencing technology (Oxford Nanopore Technologies, Oxford, UK). Previously, we developed and published an amplicon-based sequencing method in reference to CDV genome sequencing [ 51 ]. MinION library preparation, sequencing, and data analysis were performed in an identical manner.…”

“…NGS can be optimized for rapid sample preparation and real-time sequence analysis, as well as the rapid identification of certain pathogens [ 42 , 43 , 44 , 45 , 46 , 47 ]. Amplicon-based NGS sequencing is an increasingly preferred method in the rapid detection and genomic characterization of specific pathogens, with high specificity and sensitivity [ 48 , 49 , 50 , 51 , 52 ].…”