دورية أكاديمية
أعرض في EDS

Differentiation of Capripox Viruses by Nanopore Sequencing.

التفاصيل البيبلوغرافية
العنوان: Differentiation of Capripox Viruses by Nanopore Sequencing.
المؤلفون: Eltom KH; 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., Althoff AC; Division of Microbiology and Animal Hygiene, University of Goettingen, D-37077 Goettingen, Germany., Hansen S; Division of Microbiology and Animal Hygiene, University of Goettingen, D-37077 Goettingen, Germany., Böhlken-Fascher S; Division of Microbiology and Animal Hygiene, University of Goettingen, D-37077 Goettingen, Germany., Yousif A; Department of Virology, Faculty of Veterinary Medicine, Cairo University, Giza 12211, Egypt., El-Sheikh HA; Department of Infectious Diseases, Faculty of Veterinary Medicine, Zagazig University, Zagazig 44519, Egypt., ElWakeel AA; Department of Epidemiology, Veterinary Medicine Directorate, General Organization of Veterinary Services, Benha 13511, Egypt., Elgamal MA; Department of Virology, Faculty of Veterinary Medicine, Cairo University, Giza 12211, Egypt., Mossa HM; Department of Poxvirus Vaccines, Veterinary Serum and Vaccine Research Institute, Abbasia, Cairo 11517, Egypt., Aboul-Soud EA; Department of Poxvirus Vaccines, Veterinary Serum and Vaccine Research Institute, Abbasia, Cairo 11517, Egypt., Wolff J; Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald-Insel Riems, Germany., Korthase C; Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald-Insel Riems, Germany., Hoffmann B; Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald-Insel Riems, Germany., Adam NM; Department of Microbiology, Faculty of Veterinary Medicine, University of Khartoum, Shambat 13314, Khartoum North, Sudan., Abdelaziz SA; Department of Microbiology, Faculty of Veterinary Medicine, University of Khartoum, Shambat 13314, Khartoum North, Sudan., Shalaby MA; Department of Virology, Faculty of Veterinary Medicine, Cairo University, Giza 12211, Egypt., Abd El Wahed A; Division of Microbiology and Animal Hygiene, University of Goettingen, D-37077 Goettingen, Germany.; Institute of Animal Hygiene and Veterinary Public Health, Faculty of Veterinary Medicine, University of Leipzig, An den Tierkliniken 43, D-04103 Leipzig, Germany.
المصدر: Vaccines [Vaccines (Basel)] 2021 Apr 06; Vol. 9 (4). Date of Electronic Publication: 2021 Apr 06.
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: MDPI AG Country of Publication: Switzerland NLM ID: 101629355 Publication Model: Electronic Cited Medium: Print ISSN: 2076-393X (Print) Linking ISSN: 2076393X NLM ISO Abbreviation: Vaccines (Basel) Subsets: PubMed not MEDLINE
أسماء مطبوعة: Original Publication: Basel, Switzerland : MDPI AG
مستخلص: 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.
References: Epidemiol Infect. 2013 Feb;141(2):425-30. (PMID: 22717050)
BMC Vet Res. 2016 Nov 2;12(1):244. (PMID: 27806722)
J Clin Virol. 2015 Aug;69:16-21. (PMID: 26209370)
Mol Biol (Mosk). 2006 Jan-Feb;40(1):158-64. (PMID: 16523702)
Virus Genes. 2004 Aug;29(1):73-80. (PMID: 15215685)
Genome Announc. 2017 Jul 20;5(29):. (PMID: 28729259)
Trop Anim Health Prod. 1985 May;17(2):64-74. (PMID: 2411036)
J Virol Methods. 2011 Jan;171(1):134-40. (PMID: 21029751)
Arch Virol. 2019 Dec;164(12):2931-2941. (PMID: 31538254)
J Virol Methods. 2014 Apr;199:95-101. (PMID: 24462845)
Transbound Emerg Dis. 2020 Jan;67(1):80-97. (PMID: 31379093)
Viruses. 2020 Sep 28;12(10):. (PMID: 32998423)
PLoS One. 2020 May 13;15(5):e0232584. (PMID: 32401805)
Transbound Emerg Dis. 2017 Jun;64(3):729-745. (PMID: 26564428)
Transbound Emerg Dis. 2015 Oct;62(5):457-62. (PMID: 26105081)
Med Vet Entomol. 2017 Jun;31(2):150-160. (PMID: 27976815)
Epidemiol Infect. 2001 Apr;126(2):317-21. (PMID: 11349983)
EFSA J. 2018 Feb 19;16(2):e05176. (PMID: 32625811)
Br Vet J. 1991 Nov-Dec;147(6):489-503. (PMID: 1777792)
Arch Virol. 2019 Jun;164(6):1575-1585. (PMID: 30949814)
Biomol Detect Quantif. 2015 Mar;3:1-8. (PMID: 26753127)
Genome Biol. 2016 Nov 25;17(1):239. (PMID: 27887629)
BMC Genomics. 2017 Aug 10;18(1):602. (PMID: 28797240)
Curr Protoc Mol Biol. 2018 Apr;122(1):e59. (PMID: 29851291)
Vaccine. 1993 Oct;11(13):1275-9. (PMID: 8296478)
Res Vet Sci. 1986 Mar;40(2):255-8. (PMID: 3010413)
Ticks Tick Borne Dis. 2013 Jun;4(4):329-33. (PMID: 23545323)
Antiviral Res. 2014 Sep;109:1-6. (PMID: 24973760)
J Virol. 2002 Jun;76(12):6054-61. (PMID: 12021338)
Prev Vet Med. 2017 Nov 1;147:100-107. (PMID: 29254706)
J Virol. 2001 Aug;75(15):7122-30. (PMID: 11435593)
Vet World. 2016 Dec;9(12):1445-1449. (PMID: 28096619)
Trop Anim Health Prod. 2000 Aug;32(4):205-23. (PMID: 11020944)
Virol Sin. 2012 Dec;27(6):353-9. (PMID: 23271576)
فهرسة مساهمة: Keywords: capripox virus; lumpy skin disease; nanopore sequencing
تواريخ الأحداث: Date Created: 20210430 Latest Revision: 20210502
رمز التحديث: 20240628
مُعرف محوري في PubMed: PMC8067513
DOI: 10.3390/vaccines9040351
PMID: 33917413
قاعدة البيانات: MEDLINE
الوصف
تدمد:2076-393X
DOI:10.3390/vaccines9040351