Field-Adapted Full Genome Sequencing of Peste-Des-Petits-Ruminants Virus Using Nanopore Sequencing

Emeli Torsson; Tebogo Kgotlele; Gerald Misinzo; Jonas Johansson Wensman; Mikael Berg; Oskar Karlsson Lindsjö

doi:10.3389/fvets.2020.542724

Field-Adapted Full Genome Sequencing of Peste-Des-Petits-Ruminants Virus Using Nanopore Sequencing

Front Vet Sci. 2020 Oct 26:7:542724. doi: 10.3389/fvets.2020.542724. eCollection 2020.

Authors

Emeli Torsson¹, Tebogo Kgotlele², Gerald Misinzo², Jonas Johansson Wensman³, Mikael Berg¹, Oskar Karlsson Lindsjö⁴

Affiliations

¹ Department of Biomedical Sciences & Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden.
² Department of Veterinary Microbiology and Parasitology, Sokoine University of Agriculture, Morogoro, Tanzania.
³ Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden.
⁴ Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.

Abstract

Peste-des-petits-ruminants virus (PPRV) is currently the focus of a control and eradication program. Full genome sequencing has the opportunity to become a powerful tool in the eradication program by improving molecular epidemiology and the study of viral evolution. PPRV is prevalent in many resource-constrained areas, with long distances to laboratory facilities, which can lack the correct equipment for high-throughput sequencing. Here we present a protocol for near full or full genome sequencing of PPRV. The use of a portable miniPCR and MinION brings the laboratory to the field and in addition makes the production of a full genome possible within 24 h of sampling. The protocol has been successfully used on virus isolates from cell cultures and field isolates from tissue samples of naturally infected goats.

Keywords: MinION; eradication; full genome sequencing; miniPCR; molecular epidemiology; peste-des-petits-ruminants virus.