Specific capture and whole-genome phylogeography of Dolphin morbillivirus

Francesco Cerutti,Alessio Lorusso,Carla Grattarola,Cristina Casalone,Walter Mignone,Loretta Masoero,Mariella Goria,Federica Giorda,Ludovica Di Renzo,Giovanni Di Guardo,Simone Peletto,Pier Luigi Acutis,Chiara Beltramo,Nicolas Keck,Gabriella Di Francesco

doi:10.1038/s41598-020-77835-z

Abstract

Dolphin morbillivirus (DMV) is considered an emerging threat having caused several epidemics worldwide. Only few DMV genomes are publicly available. Here, we report the use of target enrichment directly from cetacean tissues to obtain novel DMV genome sequences, with sequence comparison and phylodynamic analysis. RNA from 15 tissue samples of cetaceans stranded along the Italian and French coasts (2008–2017) was purified and processed using custom probes (by bait hybridization) for target enrichment and sequenced on Illumina MiSeq. Data were mapped against the reference genome, and the novel sequences were aligned to the available genome sequences. The alignment was then used for phylogenetic and phylogeographic analysis using MrBayes and BEAST. We herein report that target enrichment by specific capture may be a successful strategy for whole-genome sequencing of DMV directly from field samples. By this strategy, 14 complete and one partially complete genomes were obtained, with reads mapping to the virus up to 98% and coverage up to 7800X. The phylogenetic tree well discriminated the Mediterranean and the NE-Atlantic strains, circulating in the Mediterranean Sea and causing two different epidemics (2008–2015 and 2014–2017, respectively), with a limited time overlap of the two strains, sharing a common ancestor approximately in 1998.

Highlights

Dolphin morbillivirus (DMV) is considered an emerging threat having caused several epidemics worldwide
Cetacean morbillivirus (CeMV) is able to infect a wide range of host species, and five different subspecies have been described so far: CeMV-1, CeMV-2, CeMV-3, CeMV-4, and CeMV-5, corresponding to Dolphin morbillivirus (DMV), Porpoise morbillivirus, the Pilot Whale morbillivirus, the Longman’s Beaked Whale morbillivirus and Guiana Dolphin morbillivirus[2,3,4,5]
Dolphin morbillivirus (DMV), to many other animal and human morbilliviruses, is a primary lymphotropic, epitheliotropic and neurotropic pathogen, which is shed outside infected cetacean hosts via the respiratory, ocular, fecal and urinary routes

Summary

Introduction

Dolphin morbillivirus (DMV) is considered an emerging threat having caused several epidemics worldwide. We report the use of target enrichment directly from cetacean tissues to obtain novel DMV genome sequences, with sequence comparison and phylodynamic analysis. We report that target enrichment by specific capture may be a successful strategy for whole-genome sequencing of DMV directly from field samples By this strategy, 14 complete and one partially complete genomes were obtained, with reads mapping to the virus up to 98% and coverage up to 7800X. Targeted enrichment of RNA or DNA of interest using custom baits is a well described procedure in gene expression profile studies, but its application is still limited in virology This approach was used to retrieve Norovirus genomes, whose sequencing is challenging due to viral genome heterogeneity, with their isolation on cell culture being troublesome[16]

Methods

Results

Conclusion