Dataset Information

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.

SUBMITTER: Ochwo S

PROVIDER: S-EPMC7035724 | biostudies-literature | 2020 Feb

REPOSITORIES: biostudies-literature

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

Ochwo Sylvester S VanderWaal Kimberly K Ndekezi Christian C Nkamwesiga Joseph J Munsey Anna A Witto Sarah Gift SG Nantima Noelina N Mayanja Franklin F Okurut Anna Rose Ademun ARA Atuhaire David Kalenzi DK Mwiine Frank Norbert FN

BMC veterinary research 20200221 1

<h4>Background</h4>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 Ugand ...[more]

PMID: 32085763

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Project description:BACKGROUND:Lumpy skin disease (LSD) is a devastating transboundary viral disease of cattle which causes significant loss in production. Although this disease has been reported in Uganda and throughout East Africa, there is almost no information about its epidemiology, spatial or spatio-temporal distribution. We carried out a retrospective study on the epidemiology of LSD in Uganda between the years 2002 and 2016, using data on reported outbreaks collected monthly by the central government veterinary administration. Descriptive statistics were computed on frequency of outbreaks, number of cases, vaccinations and deaths. We evaluated differences in the number of reported outbreaks across different regions (agro-ecological zones), districts, months and years. Spatial, temporal and space-time scan statistics were used to identify possible epidemiological clusters of LSD outbreaks. RESULTS:A total of 1161 outbreaks and 319,355 cases of LSD were reported from 55 out of 56 districts of Uganda. There was a significant difference in incidence between years (P?=?0.007) and across different regions. However, there was no significant difference in the number of outbreaks per month (P?=?0.443). The Central region reported the highest number of outbreaks (n?=?418, 36%) followed by Eastern (n?=?372, 32%), Southwestern (n?=?140, 12%), Northern (n?=?131, 11%), Northeastern (n?=?37, 3%), Western (n?=?41, 4%) and Northwestern (n?=?22, 2%) regions. Several endemic hotspots for the circulation of LSD were identified in the Central and Eastern regions using spatial cluster analyses. Outbreaks in endemic hotspots were less seasonal and had strikingly lower mortality and case-fatality rates than the other regions, suggesting an underlying difference in the epidemiology and impact of LSD in these different zones. CONCLUSION:Lumpy Skin disease is endemic in Uganda, with outbreaks occurring annually in all regions of the country. We identified potential spatial hotspots for LSD outbreaks, underlining the need for risk-based surveillance to establish the actual disease prevalence and risk factors for disease maintenance. Space-time analysis revealed that sporadic LSD outbreaks tend to occur both within and outside of endemic areas. The findings from this study will be used as a baseline for further epidemiological studies for the development of sustainable programmes towards the control of LSD in Uganda.

Project description:BackgroundLumpy skin disease (LSD) is endemic in Egypt despite the Egyptian authorities' annual mass vaccination of cattle with sheeppox vaccine (Veterinary Serum and Vaccine Research Institute, Egypt), and the LSD virus (LSDV) continues to thrive practically every summer. The disease has a huge economic impact on the trade of the animal and its by-product.AimThis paper study the molecular characterization of LSDV strains that have been circulating in Sharkia Governorate, Egypt, for three successive years (2018, 2019, and 2020).MethodsA total of 61 specimens (26 skin nodules and 35 oculonasal swabs) were collected from a clinic in the hospital of veterinary medicine, Zagazig University, during the summer months (July, August, and September) of three outbreaks in 2018, 2019, and 2020. These were examined by polymerase chain reaction (PCR) based on the open reading frame 103 (ORF103) gene to confirm the suspected cases and determine the degree of homology between the three different outbreaks during three successive years between each other and between the derived sequences of GenBank.ResultsCattle is thought to be infected with LSDV due to the presence of scattered local or diffuse circumscribed skin nodules along with fever and lymph node enlargement and sometimes leg edema. The PCR approach proved rapid, sensitive, and specific for the detection of LSDV and confirmative diagnosis of the disease. Forty-six were detected to be positive by PCR (75.4%). The seven sequenced samples were translated to amino acid and registered in GenBank under accession number MW357655-MW357661. A single nucleotide mutation and amino acid variation were observed at positions 161 C (2020)/T (2018&2019) and consequently, a change in the amino acid at position 54 P (2020)/L (2018&2019) between the outbreak in 2020 and those in 2018 and 2019, respectively. The field LSDV isolates from Egypt cattle were more closely related to other LSDV sequences from Africa (Kenya), Asia, Europe, and the United States.These findings highlight the necessity of ongoing surveillance and characterization of circulating strains and the need to improve procedures for distinguishing vaccine strains from field viruses.

Project description:BackgroundAfrican swine fever (ASF) is a highly lethal and economically significant disease of domestic pigs in Eastern Africa particularly in Uganda where outbreaks regularly occur. Sequence analysis of variable genome regions have been extensively used for molecular epidemiological studies of African swine fever virus (ASFV) isolates. By combining p72, P54 and pB602L (CVR), a high level resolution approach is achieved for viral discrimination. The major aim of this study therefore, was to investigate the genetic relatedness of ASF outbreaks that occurred between 2010 and 2013 in Uganda to contribute to the clarification of the epidemiological situation over a four year period.MethodsTissue samples from infected domestic pigs associated with an ASF outbreak from 15 districts in Uganda were confirmed as being infected with ASFV using a p72 gene-based polymerase chain reaction amplification (PCR) assay recommended by OIE. The analysis was conducted by genotyping based on sequence data from three single copy ASFV genes. The E183L gene encoding the structural protein P54 and part of the gene encoding the p72 protein was used to delineate genotypes. Intra-genotypic resolution of viral relationships was achieved by analysis of tetramer amino acid repeats within the hypervariable CVR of the B602L gene.ResultsTwenty one (21) ASF outbreaks were confirmed by the p72 ASF diagnostic PCR, however; only 17 isolates were successfully aligned after sequencing. Our entire isolates cluster with previous ASF viruses in genotype IX isolated in Uganda and Kenya using p72 and P54 genes. Analysis of the CVR gene generated three sub-groups one with 23 tetrameric amino acid repeats (TRS) with an additional CAST sequence, the second with 22 TRS while one isolate Ug13. Kampala1 had 13 TRS.ConclusionWe identified two new CVR subgroups different from previous studies. This study constitutes the first detailed assessment of the molecular epidemiology of ASFV in domestic pigs in the different regions of Uganda.

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

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

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