Differentiation of Capripox Viruses by Nanopore Sequencing
Kamal H. Eltom,
Anna Christina Althoff,
Sören Hansen,
Susanne Böhlken-Fascher,
Ausama Yousif,
Hussein A. El-Sheikh,
Ahmed A. ElWakeel,
Mahmoud A. Elgamal,
Hadeer M. Mossa,
Emad A. Aboul-Soud,
Janika Wolff,
Christian Korthase,
Bernd Hoffmann,
Nabawia M. Adam,
Sanaa A. Abdelaziz,
Mohamed A. Shalaby,
Ahmed Abd El Wahed
Affiliations
Kamal H. Eltom
Unit of Animal Health and Safety of Animal Products, Institute for Studies and Promotion of Animal Exports, University of Khartoum, Shambat 13314, Khartoum North, Sudan
Anna Christina Althoff
Division of Microbiology and Animal Hygiene, University of Goettingen, D-37077 Goettingen, Germany
Sören Hansen
Division of Microbiology and Animal Hygiene, University of Goettingen, D-37077 Goettingen, Germany
Susanne Böhlken-Fascher
Division of Microbiology and Animal Hygiene, University of Goettingen, D-37077 Goettingen, Germany
Ausama Yousif
Department of Virology, Faculty of Veterinary Medicine, Cairo University, Giza 12211, Egypt
Hussein A. El-Sheikh
Department of Infectious Diseases, Faculty of Veterinary Medicine, Zagazig University, Zagazig 44519, Egypt
Ahmed A. ElWakeel
Department of Epidemiology, Veterinary Medicine Directorate, General Organization of Veterinary Services, Benha 13511, Egypt
Mahmoud A. Elgamal
Department of Virology, Faculty of Veterinary Medicine, Cairo University, Giza 12211, Egypt
Hadeer M. Mossa
Department of Poxvirus Vaccines, Veterinary Serum and Vaccine Research Institute, Abbasia, Cairo 11517, Egypt
Emad A. Aboul-Soud
Department of Poxvirus Vaccines, Veterinary Serum and Vaccine Research Institute, Abbasia, Cairo 11517, Egypt
Janika Wolff
Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald-Insel Riems, Germany
Christian Korthase
Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald-Insel Riems, Germany
Bernd Hoffmann
Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald-Insel Riems, Germany
Nabawia M. Adam
Department of Microbiology, Faculty of Veterinary Medicine, University of Khartoum, Shambat 13314, Khartoum North, Sudan
Sanaa A. Abdelaziz
Department of Microbiology, Faculty of Veterinary Medicine, University of Khartoum, Shambat 13314, Khartoum North, Sudan
Mohamed A. Shalaby
Department of Virology, Faculty of Veterinary Medicine, Cairo University, Giza 12211, Egypt
Ahmed Abd El Wahed
Division of Microbiology and Animal Hygiene, University of Goettingen, D-37077 Goettingen, Germany
The genus capripoxvirus (CaPV), family Poxviridae, includes three virus species: goatpox virus (GPV), sheeppox virus (SPV) and lumpy skin disease virus (LSDV). CaPV causes disease outbreaks with consequent economic losses in Africa and the Middle East. LSDV has recently spread to Southeast Europe. As CaPVs share 96–97% genetic similarity along the length of the entire genome and are difficult to distinguish using serological assays, simple, reliable and fast methods for diagnosis and species differentiation are crucial in cases of disease outbreak. The present study aimed to develop a field-applicable CaPV differentiation method. Nanopore technology was used for whole genome sequencing. A local database of complete CaPV genomes and partial sequences of three genes (RPO30, P32 and GPCR) was established for offline Basic Local Alignment Search Tool (BLAST). Specificities of 98.04% in whole genome and 97.86% in RPO30 gene runs were obtained among the three virus species, while other databases were less specific. The total run time was shortened to approximately 2 h. Functionality of the developed procedure was proved by samples with high host background sequences. Reliable differentiation options for the quality and capacity of hardware, and sample quality of suspected cases, were derived from these findings. The whole workflow can be performed rapidly with a mobile suitcase laboratory and mini-computer, allowing application at the point-of-need with limited resource settings.
