A Standardized Pipeline for Assembly and Annotation of African Swine Fever Virus Genome-Reference-Cited by-同舟云学术

A Standardized Pipeline for Assembly and Annotation of African Swine Fever Virus Genome

Published:2024-08-13 Issue:8 Volume:16 Page:1293
ISSN:1999-4915
Container-title:Viruses
language:en
Short-container-title:Viruses

Author:

Spinard Edward¹²^ORCID,Dinhobl Mark¹²,Erdelyan Cassidy N. G.³^ORCID,O’Dwyer James⁴,Fenster Jacob⁵,Birtley Hillary⁵,Tesler Nicolas⁵^ORCID,Calvelage Sten⁶^ORCID,Leijon Mikael⁷^ORCID,Steinaa Lucilla⁸^ORCID,O’Donnell Vivian⁹^ORCID,Blome Sandra⁶^ORCID,Bastos Armanda¹⁰^ORCID,Ramirez-Medina Elizabeth¹²,Lacasta Anna⁸^ORCID,Ståhl Karl¹¹^ORCID,Qiu Huaji¹²^ORCID,Nilubol Dachrit¹³,Tennakoon Chandana¹⁴,Maesembe Charles¹⁵^ORCID,Faburay Bonto⁹,Ambagala Aruna⁴^ORCID,Williams David³^ORCID,Ribeca Paolo¹⁶¹⁷,Borca Manuel V.¹²,Gladue Douglas P.¹²

Affiliation:

1. 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

2. U.S. Department of Agriculture, Agricultural Research Service, Foreign Animal Disease Research Unit, National Bio and Agro-Defense Facility, Manhattan, KS 66502, USA

3. CSIRO, Australian Centre for Disease Preparedness, Geelong, VIC 3220, Australia

4. National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3M4, Canada

5. Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, TN 37830, USA

6. Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald-Insel Riems, Germany

7. Department of Microbiology, Swedish Veterinary Agency, SE-751 89 Uppsala, Sweden

8. Animal and Human Heath Program, International Livestock Research Institute, Nairobi 00100, Kenya

9. U.S. Department of Agriculture, Animal and Plant Inspection Service, Plum Island Animal Disease Center, Greenport, NY 11944, USA

10. Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Onderstepoort 0110, South Africa

11. Department of Epidemiology, Surveillance and Risk assessment, Swedish Veterinary Agency, SE-751 89 Uppsala, Sweden

12. 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

13. 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

14. The Pirbright Institute, Ash Road, Pirbright, Woking GU24 0NF, UK

15. Department of Zoology, Entomology and Fisheries Sciences, School of Biosciences, College of Natural Sciences, Makerere University, Kampala P.O. Box 7062, Uganda

16. UK Health Security Agency, London E14 4PU, UK

17. Biomathematics and Statistics Scotland, Edinburgh EH9 3FD, UK

Abstract

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.

Funder

USDA

Core Capability

Publisher

MDPI AG

Link

https://www.mdpi.com/1999-4915/16/8/1293/pdf

Reference41 articles.

1. Genomic analysis of highly virulent Georgia 2007/1 isolate of African swine fever virus;Chapman;Emerg. Infect. Dis.,2011

2. Detection of Recombinant African Swine Fever Virus Strains of p72 Genotypes I and II in Domestic Pigs, Vietnam, 2023;Le;Emerg. Infect. Dis.,2024

3. Highly lethal genotype I and II recombinant African swine fever viruses detected in pigs;Zhao;Nat. Commun.,2023

4. Carriquiry, M., Elobeid, A., Swenson, D., and Hayes, D. (2020). Impacts of African Swine Fever in Iowa and the United States, Center for Agricultural and Rural Development.

5. Genotyping field strains of African swine fever virus by partial p72 gene characterisation;Bastos;Arch. Virol.,2003