A Standardized Pipeline for Assembly and Annotation of African Swine Fever Virus Genome
Edward Spinard,
Mark Dinhobl,
Cassidy N. G. Erdelyan,
James O’Dwyer,
Jacob Fenster,
Hillary Birtley,
Nicolas Tesler,
Sten Calvelage,
Mikael Leijon,
Lucilla Steinaa,
Vivian O’Donnell,
Sandra Blome,
Armanda Bastos,
Elizabeth Ramirez-Medina,
Anna Lacasta,
Karl Ståhl,
Huaji Qiu,
Dachrit Nilubol,
Chandana Tennakoon,
Charles Maesembe,
Bonto Faburay,
Aruna Ambagala,
David Williams,
Paolo Ribeca,
Manuel V. Borca,
Douglas P. Gladue
Affiliations
Edward Spinard
U.S. Department of Agriculture, Agricultural Research Service, Foreign Animal Disease Research Unit, Plum Island Animal Disease Center (PIADC), P.O. Box 848, Greenport, NY 11944, USA
Mark Dinhobl
U.S. Department of Agriculture, Agricultural Research Service, Foreign Animal Disease Research Unit, Plum Island Animal Disease Center (PIADC), P.O. Box 848, Greenport, NY 11944, USA
Cassidy N. G. Erdelyan
CSIRO, Australian Centre for Disease Preparedness, Geelong, VIC 3220, Australia
James O’Dwyer
National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3M4, Canada
Jacob Fenster
Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, TN 37830, USA
Hillary Birtley
Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, TN 37830, USA
Nicolas Tesler
Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, TN 37830, USA
Sten Calvelage
Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald-Insel Riems, Germany
Mikael Leijon
Department of Microbiology, Swedish Veterinary Agency, SE-751 89 Uppsala, Sweden
Lucilla Steinaa
Animal and Human Heath Program, International Livestock Research Institute, Nairobi 00100, Kenya
Vivian O’Donnell
U.S. Department of Agriculture, Animal and Plant Inspection Service, Plum Island Animal Disease Center, Greenport, NY 11944, USA
Sandra Blome
Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald-Insel Riems, Germany
Armanda Bastos
Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Onderstepoort 0110, South Africa
Elizabeth Ramirez-Medina
U.S. Department of Agriculture, Agricultural Research Service, Foreign Animal Disease Research Unit, Plum Island Animal Disease Center (PIADC), P.O. Box 848, Greenport, NY 11944, USA
Anna Lacasta
Animal and Human Heath Program, International Livestock Research Institute, Nairobi 00100, Kenya
Karl Ståhl
Department of Epidemiology, Surveillance and Risk assessment, Swedish Veterinary Agency, SE-751 89 Uppsala, Sweden
Huaji Qiu
State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 100081, China
Dachrit Nilubol
Swine Viral Evolution and Vaccine Development Research Unit, Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Henry Dunant Road, Pathumwan, Bangkok 10330, Thailand
Chandana Tennakoon
The Pirbright Institute, Ash Road, Pirbright, Woking GU24 0NF, UK
Charles Maesembe
Department of Zoology, Entomology and Fisheries Sciences, School of Biosciences, College of Natural Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
Bonto Faburay
U.S. Department of Agriculture, Animal and Plant Inspection Service, Plum Island Animal Disease Center, Greenport, NY 11944, USA
Aruna Ambagala
National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3M4, Canada
David Williams
CSIRO, Australian Centre for Disease Preparedness, Geelong, VIC 3220, Australia
Paolo Ribeca
UK Health Security Agency, London E14 4PU, UK
Manuel V. Borca
U.S. Department of Agriculture, Agricultural Research Service, Foreign Animal Disease Research Unit, Plum Island Animal Disease Center (PIADC), P.O. Box 848, Greenport, NY 11944, USA
Douglas P. Gladue
U.S. Department of Agriculture, Agricultural Research Service, Foreign Animal Disease Research Unit, Plum Island Animal Disease Center (PIADC), P.O. Box 848, Greenport, NY 11944, USA
Obtaining a complete good-quality sequence and annotation for the long double-stranded DNA genome of the African swine fever virus (ASFV) from next-generation sequencing (NGS) technology has proven difficult, despite the increasing availability of reference genome sequences and the increasing affordability of NGS. A gap analysis conducted by the global African swine fever research alliance (GARA) partners identified that a standardized, automatic pipeline for NGS analysis was urgently needed, particularly for new outbreak strains. Whilst there are several diagnostic and research labs worldwide that collect isolates of the ASFV from outbreaks, many do not have the capability to analyze, annotate, and format NGS data from outbreaks for submission to NCBI, and some publicly available ASFV genomes have missing or incorrect annotations. We developed an automated, standardized pipeline for the analysis of NGS reads that directly provides users with assemblies and annotations formatted for their submission to NCBI. This pipeline is freely available on GitHub and has been tested through the GARA partners by examining two previously sequenced ASFV genomes; this study also aimed to assess the accuracy and limitations of two strategies present within the pipeline: reference-based (Illumina reads) and de novo assembly (Illumina and Nanopore reads) strategies.
