Molecular detection and phylogenetic analysis of lumpy skin disease virus from outbreaks in Uganda 2017–2018

Abstract

Background: Lumpy skin disease (LSD) is an infectious viral disease of cattle caused by a Capripoxvirus. LSD has substantial economic implications, with infection resulting in permanent damage to the skin of affected animals which lowers their commercial value. In Uganda, LSD is endemic and cases of the disease are frequently reported to government authorities. This study was undertaken to molecularly characterize lumpy skin disease virus (LSDV) strains that have been circulating in Uganda between 2017 and 2018. Secondly, the study aimed to determine the phylogenetic relatedness of Ugandan LSDV sequences with published sequences, available in GenBank. Results: A total of 7 blood samples and 16 skin nodule biopsies were screened for LSDV using PCR to confirm presence of LSDV nucleic acids. PCR positive samples were then characterised by amplifying the GPCR gene. These amplified genes were sequenced and phylogenetic trees were constructed. Out of the 23 samples analysed, 15 were positive for LSDV by PCR (65.2%). The LSDV GPCR sequences analysed contained the unique signatures of LSDV (A11, T12, T34, S99, and P199) which further confirmed their identity. Sequence comparison with vaccine strains revealed a 12 bp deletion unique to Ugandan outbreak strains. Phylogenetic analysis indicated that the LSDV sequences from this study clustered closely with sequences from neighboring East African countries and with LSDV strains from recent outbreaks in Europe. It was noted that the sequence diversity amongst LSDV strains from Africa was higher than diversity from Eurasia. Conclusion: The LSDV strains circulating in Uganda were closely related with sequences from neighboring African countries and from Eurasia. Comparison of the GPCR gene showed that outbreak strains differed from vaccine strains. This information is necessary to understand LSDV molecular epidemiology and to contribute knowledge towards the development of control strategies by the Government of Uganda.

Genetic and phylogenetic analysis of lumpy skin disease viruses (LSDV) isolated from the first and subsequent field outbreaks in India during 2019 reveals close proximity with unique signatures of historical Kenyan NI‐2490/Kenya/KSGP‐like field strains

“…The genetic and phylogenetic analyses of four complete genes (GPCR, RPO30, P32 and EEV) revealed that LSDVs from 2019 outbreaks in niotaki et al, 2017;Gelaye et al, 2015;Le Goff et al, 2009;Ochwo et al, 2020;Sevik & Dogan, 2017;Tuppurainen et al, 2014 O-240 vaccine strain and the attenuated KS-1 and Kenyavac strains are all LSDV (Biswas et al, 2020;Lamien et al, 2011b, Tuppurainen et al, 2014Tulman et al, 2002). In fact, the full genome sequence analysis has recently revealed that NI-2490, Kenya and KSGP O-240 (Kenyavac) strains are very closely related with only one significant difference between these three LSDV genomes (Biswas et al, 2020).…”

Spatio-temporal patterns of lumpy skin disease outbreaks in dairy farms in northeastern Thailand

“…Although STP and Poisson models have been used in previous studies ( 23 , 40 ), the use of the Bernoulli model for analyzing LSD outbreak data is very limited. In fact, the application of Bernoulli model to LSD outbreak data provides some advantages ( 41 , 42 ).…”

Genetic Evidence of Multiple Introductions of Lumpy Skin Disease Virus into Saratov Region, Russia

“…In fact, serological identification followed by differentiation with intra-specific typing is not possible due to dramatic cross-reactions between LSDV, SPPV and GTPV as the strains of CapPVs were found to be antigenically indistinguishable [21]. Since both SPPV and LSDV are phylogenetically distinct and could be differentiated using molecular tools available [1][2][3][4]35], the individual DNA from clinical specimens of Case1 and Case2 animals were carefully investigated. For this purpose, the coding region of the CapPV GPCR gene was determined according to the recommendation of Le Goff et al [4], which has been used worldwide for successful CapPVs intra-specific differentiation.…”

“…In fact, a phylogenetic analysis based on the nucleic acid sequences of CapPVs isolates using the Neighbor-Joining algorithm showed three separate genetic clusters consisting of LSDV, GTPV and SPPV lineages [4]. Moreover, a certain intra-group diversity in the LSDV cluster was revealed [4,22,24,31,[33][34][35][36][37][38][39][40].…”

“…Furthermore, a phylogenetic analysis clustered LSDV wild field outbreak-related isolates, vaccine and the so-called 'vaccine-like' strains into separate clades within the Capripoxvirus family [31,[35][36][37][38][39][40].…”