PMID- 33917413
OWN - NLM
STAT- PubMed-not-MEDLINE
LR  - 20210502
IS  - 2076-393X (Print)
IS  - 2076-393X (Electronic)
IS  - 2076-393X (Linking)
VI  - 9
IP  - 4
DP  - 2021 Apr 6
TI  - Differentiation of Capripox Viruses by Nanopore Sequencing.
LID - 10.3390/vaccines9040351 [doi]
LID - 351
AB  - 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.
FAU - Eltom, Kamal H
AU  - Eltom KH
AUID- ORCID: 0000-0002-3707-5087
AD  - 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.
FAU - Althoff, Anna Christina
AU  - Althoff AC
AD  - Division of Microbiology and Animal Hygiene, University of Goettingen, D-37077 
      Goettingen, Germany.
FAU - Hansen, Soren
AU  - Hansen S
AD  - Division of Microbiology and Animal Hygiene, University of Goettingen, D-37077 
      Goettingen, Germany.
FAU - Bohlken-Fascher, Susanne
AU  - Bohlken-Fascher S
AD  - Division of Microbiology and Animal Hygiene, University of Goettingen, D-37077 
      Goettingen, Germany.
FAU - Yousif, Ausama
AU  - Yousif A
AUID- ORCID: 0000-0003-3782-0435
AD  - Department of Virology, Faculty of Veterinary Medicine, Cairo University, Giza 
      12211, Egypt.
FAU - El-Sheikh, Hussein A
AU  - El-Sheikh HA
AD  - Department of Infectious Diseases, Faculty of Veterinary Medicine, Zagazig 
      University, Zagazig 44519, Egypt.
FAU - ElWakeel, Ahmed A
AU  - ElWakeel AA
AUID- ORCID: 0000-0002-1046-3127
AD  - Department of Epidemiology, Veterinary Medicine Directorate, General Organization 
      of Veterinary Services, Benha 13511, Egypt.
FAU - Elgamal, Mahmoud A
AU  - Elgamal MA
AD  - Department of Virology, Faculty of Veterinary Medicine, Cairo University, Giza 
      12211, Egypt.
FAU - Mossa, Hadeer M
AU  - Mossa HM
AD  - Department of Poxvirus Vaccines, Veterinary Serum and Vaccine Research Institute, 
      Abbasia, Cairo 11517, Egypt.
FAU - Aboul-Soud, Emad A
AU  - Aboul-Soud EA
AD  - Department of Poxvirus Vaccines, Veterinary Serum and Vaccine Research Institute, 
      Abbasia, Cairo 11517, Egypt.
FAU - Wolff, Janika
AU  - Wolff J
AD  - Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research 
      Institute for Animal Health, Sudufer 10, 17493 Greifswald-Insel Riems, Germany.
FAU - Korthase, Christian
AU  - Korthase C
AD  - Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research 
      Institute for Animal Health, Sudufer 10, 17493 Greifswald-Insel Riems, Germany.
FAU - Hoffmann, Bernd
AU  - Hoffmann B
AUID- ORCID: 0000-0001-5358-6445
AD  - Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research 
      Institute for Animal Health, Sudufer 10, 17493 Greifswald-Insel Riems, Germany.
FAU - Adam, Nabawia M
AU  - Adam NM
AD  - Department of Microbiology, Faculty of Veterinary Medicine, University of 
      Khartoum, Shambat 13314, Khartoum North, Sudan.
FAU - Abdelaziz, Sanaa A
AU  - Abdelaziz SA
AD  - Department of Microbiology, Faculty of Veterinary Medicine, University of 
      Khartoum, Shambat 13314, Khartoum North, Sudan.
FAU - Shalaby, Mohamed A
AU  - Shalaby MA
AD  - Department of Virology, Faculty of Veterinary Medicine, Cairo University, Giza 
      12211, Egypt.
FAU - Abd El Wahed, Ahmed
AU  - Abd El Wahed A
AUID- ORCID: 0000-0003-3347-6075
AD  - Division of Microbiology and Animal Hygiene, University of Goettingen, D-37077 
      Goettingen, Germany.
AD  - Institute of Animal Hygiene and Veterinary Public Health, Faculty of Veterinary 
      Medicine, University of Leipzig, An den Tierkliniken 43, D-04103 Leipzig, 
      Germany.
LA  - eng
PT  - Journal Article
DEP - 20210406
PL  - Switzerland
TA  - Vaccines (Basel)
JT  - Vaccines
JID - 101629355
PMC - PMC8067513
OTO - NOTNLM
OT  - capripox virus
OT  - lumpy skin disease
OT  - nanopore sequencing
COIS- The authors declare no conflict of interest.
EDAT- 2021/05/01 06:00
MHDA- 2021/05/01 06:01
PMCR- 2021/04/06
CRDT- 2021/04/30 01:06
PHST- 2021/02/28 00:00 [received]
PHST- 2021/03/29 00:00 [revised]
PHST- 2021/03/29 00:00 [accepted]
PHST- 2021/04/30 01:06 [entrez]
PHST- 2021/05/01 06:00 [pubmed]
PHST- 2021/05/01 06:01 [medline]
PHST- 2021/04/06 00:00 [pmc-release]
AID - vaccines9040351 [pii]
AID - vaccines-09-00351 [pii]
AID - 10.3390/vaccines9040351 [doi]
PST - epublish
SO  - Vaccines (Basel). 2021 Apr 6;9(4):351. doi: 10.3390/vaccines9040351.