scholarly journals Use of an Alignment-Free Method for the Geographical Discrimination of GTPVs Based on the GPCR Sequences

2021 ◽  
Vol 9 (4) ◽  
pp. 855
Author(s):  
Tesfaye Rufael Chibssa ◽  
Yang Liu ◽  
Melaku Sombo ◽  
Jacqueline Kasiiti Lichoti ◽  
Janchivdorj Erdenebaatar ◽  
...  
Keyword(s):  
Lumpy Skin Disease ◽  
Alignment Free ◽  
Central Asian ◽  
Source Tracing ◽  
Geographical Regions ◽  
Gpcr Gene ◽  
Geographical Discrimination ◽  
Sequence Profiles ◽  
G Protein Coupled ◽  
Effective Source

Goatpox virus (GTPV) belongs to the genus Capripoxvirus, together with sheeppox virus (SPPV) and lumpy skin disease virus (LSDV). GTPV primarily affects sheep, goats and some wild ruminants. Although GTPV is only present in Africa and Asia, the recent spread of LSDV in Europe and Asia shows capripoxviruses could escape their traditional geographical regions to cause severe outbreaks in new areas. Therefore, it is crucial to develop effective source tracing of capripoxvirus infections. Earlier, conventional phylogenetic methods, based on limited samples, identified three different nucleotide sequence profiles in the G-protein-coupled chemokine receptor (GPCR) gene of GTPVs. However, this method did not differentiate GTPV strains by their geographical origins. We have sequenced the GPCR gene of additional GTPVs and analyzed them with publicly available sequences, using conventional alignment-based methods and an alignment-free approach exploiting k-mer frequencies. Using the alignment-free method, we can now classify GTPVs based on their geographical origin: African GTPVs and Asian GTPVs, which further split into Western and Central Asian (WCA) GTPVs and Eastern and Southern Asian (ESA) GTPVs. This approach will help determine the source of introduction in GTPV emergence in disease-free regions and detect the importation of additional strains in disease-endemic areas.

scholarly journals Lumpy skin disease in Kazakhstan

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Mukhit B. Orynbayev ◽  
Raikhan K. Nissanova ◽  
Berik M. Khairullin ◽  
Arman Issimov ◽  
Kunsulu D. Zakarya ◽  
...  
Keyword(s):  
Disease Virus ◽  
Cell Cultures ◽  
Skin Disease ◽  
Stomoxys Calcitrans ◽  
Lumpy Skin Disease ◽  
Dermacentor Marginatus ◽  
The Third ◽  
Gpcr Gene ◽  
Mdbk Cells ◽  
The Republic

AbstractThis study describes the registration of the first cases of lumpy skin disease in July 2016 in the Republic of Kazakhstan. In the rural district of Makash, Kurmangazinsky district of Atyrau region, 459 cattle fell ill and 34 died (morbidity 12.9% and mortality 0.96%). To determine the cause of the disease, samples were taken from sick and dead animals, as well as from insects and ticks. LSDV DNA was detected by PCR in all samples from dead animals and ticks (Dermacentor marginatus and Hyalomma asiaticum), in 14.29% of samples from horseflies (Tabanus bromius), and in one of the samples from two Stomoxys calcitrans flies. The reproductive LSD virus was isolated from organs of dead cattle and insects in the culture of LT and MDBK cells. The virus accumulated in cell cultures of LT and MDBK at the level of the third passage with titers in the range of 5.5–5.75 log 10 TCID50/cm3. Sequencing of the GPCR gene allowed us to identify this virus as a lumpy skin disease virus.

scholarly journals PO 8468 DETERMINE TB–LAM LATERAL FLOW ASSAY: DOES M. TUBERCULOSIS LINEAGE INFLUENCE ITS PERFORMANCE?

2019 ◽  
Vol 4 (Suppl 3) ◽  
pp. A41.1-A41
Author(s):  
Willy Ssengooba ◽  
Lydia Nakiyingi ◽  
Joloba Moses
Keyword(s):  
Lateral Flow ◽  
Hiv Positive ◽  
Blood Samples ◽  
Asian Strain ◽  
Central Asian ◽  
Mulago National Referral Hospital ◽  
Geographical Regions ◽  
Accuracy Study ◽  
Tb Diagnostics ◽  
National Referral Hospital

BackgroundAmong HIV-positive individuals with CD4 ≤100 cells/mm3, M. tuberculosis (Mtb) bacteraemia is associated with a positive tuberculosis urine lipoarabinomannan (LAM) test. We conducted a retrospective study, to determine the effect of Mtb lineage on the performance of the Determine TB LAM lateral flow (LF-LAM) assay.MethodsThis was nested in a prospective TB diagnostics accuracy study among HIV-positive presumptive TB patients from Mulago National Referral Hospital, Kampala, Uganda, including both inpatients and outpatients. We considered data of 51 HIV-positive individuals with both pulmonary and Mtb bacteraemia. We also evaluated the effect of having mixed Mtb strains using both spoligotyping and MIRU-VNTR 24 loci methods.ResultsLF-LAM was; negative among 4 (7.8%; 95% CI, 2.17% to 18.8%), positive among 39 (76.5%; 95% CI, 62.5% to 87.2%) and indeterminate among 8 (15.7%; 95% CI, 7.0% to 28.5%) participants. Mtb lineages from blood samples were: Central Asian Strain (CAS; L3) 10/51 (19.6%) and Euro-American lineage (L4) 41/51 (80.4%). Mtb lineages from sputum samples were 7/51 (13.7%) L3 and 44/51 (86.3%) were L4. Among participants with L3 in blood, LFLAM was positive in 9 (90%; 95% CI, 55.4%–99.7%) whereas those with L4, LF-LAM was positive among 30 (73.2% 95% CI, 57.0% to 85.7%). For those with L3 in sputum, LF-LAM was positive among 7 (100%) and those with L4 was 32 (72.7%; 95% CI 57.2% to 85.0%). Two participants had mixed Mtb strains (all L4) and all LF-LAM positive (2+ and 4+).ConclusionOur study shows that M. tuberculosis lineage 3 may have more sensitivity to LF-LAM assay than lineage 4. The high number of indeterminate results with L4 requires more investigations. Our findings suggest that LF-LAM performance may differ by geographical regions depending on the dominant M. tuberculosis lineage.

Alignment-Free Classification of G-Protein-Coupled Receptors Using Self-Organizing Maps

2006 ◽  
Vol 46 (3) ◽  
pp. 1479-1490 ◽  
Author(s):  
Joji M. Otaki ◽  
Akihito Mori ◽  
Yoshimasa Itoh ◽  
Takashi Nakayama ◽  
Haruhiko Yamamoto
Keyword(s):  
G Protein ◽  
G Protein Coupled Receptors ◽  
Self Organizing Maps ◽  
Alignment Free ◽  
Free Classification ◽  
G Protein Coupled ◽  
Self Organizing

scholarly journals Molecular detection and phylogenetic analysis of Lumpy skin disease virus from outbreaks in Uganda 2017-2018

2019 ◽  
Author(s):  
Sylvester Ochwo ◽  
Kimberly Vanderwaal ◽  
Christian Ndekezi ◽  
Joseph Nkamwesiga ◽  
Anna Munsey ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Disease Virus ◽  
Skin Disease ◽  
Phylogenetic Trees ◽  
African Countries ◽  
Economic Implications ◽  
Lumpy Skin Disease ◽  
Lumpy Skin Disease Virus ◽  
Gpcr Gene ◽  
The Government

Abstract Background Lumpy skin disease (LSD) is an infectious viral disease of cattle caused by a capripox virus. 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 acid. 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 12bp 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 countries. Comparison of GPCR gene showed that vaccine strains were not responsible for outbreaks. This means that vaccination with the currently used vaccine will probably be effective for the control of LSD in Uganda. This information is necessary to understand LSDV molecular epidemiology and to contribute knowledge towards the development of more appropriate control strategies by the Government of Uganda.

scholarly journals Molecular detection and phylogenetic analysis of Lumpy skin disease virus from outbreaks in Uganda 2017-2018

2020 ◽  
Author(s):  
Sylvester Ochwo ◽  
Kimberly VanderWaal ◽  
Christian Ndekezi ◽  
Joseph Nkamwesiga ◽  
Anna Munsey ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Disease Virus ◽  
Skin Disease ◽  
Phylogenetic Trees ◽  
African Countries ◽  
Economic Implications ◽  
Lumpy Skin Disease ◽  
Lumpy Skin Disease Virus ◽  
Gpcr Gene ◽  
The Government

Abstract Background: Lumpy skin disease (LSD) is an infectious viral disease of cattle caused by a Capripox virus. 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 characterized by amplifying the GPCR gene. These amplified genes were sequenced and phylogenetic trees were constructed. Out of the 23 samples analyzed, 15 were positive for LSDV by PCR (65.2%). The LSDV GPCR sequences analyzed contained the unique signatures of LSDV (A11, T12, T34, S99, and P199) which further confirmed their identity. Sequence comparison with vaccine strains revealed a 12bp 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.

scholarly journals Capripoxvirus G-protein-coupled chemokine receptor: a host-range gene suitable for virus animal origin discrimination

2009 ◽  
Vol 90 (8) ◽  
pp. 1967-1977 ◽  
Author(s):  
Christian Le Goff ◽  
Charles Euloge Lamien ◽  
Emna Fakhfakh ◽  
Amélie Chadeyras ◽  
Elexpeter Aba-Adulugba ◽  
...  
Keyword(s):  
Host Range ◽  
G Protein ◽  
Chemokine Receptor ◽  
Skin Disease ◽  
Animal Origin ◽  
Lumpy Skin Disease ◽  
Gpcr Gene ◽  
Genetic Clusters ◽  
Host Origin ◽  
Group Diversity

The genus Capripoxvirus within the family Poxviridae comprises three closely related viruses, namely goat pox, sheep pox and lumpy skin disease viruses. This nomenclature is based on the animal species from which the virus was first isolated, respectively, goat, sheep and cattle. Since capripoxviruses are serologically identical, their specific identification relies exclusively on the use of molecular tools. We describe here the suitability of the G-protein-coupled chemokine receptor (GPCR) gene for use in host-range grouping of capripoxviruses. The analysis of 58 capripoxviruses showed three tight genetic clusters consisting of goat pox, sheep pox and lumpy skin disease viruses. However, a few discrepancies exist with the classical virus–host origin nomenclature: a virus isolated from sheep is grouped in the goat poxvirus clade and vice versa. Intra-group diversity was further observed for the goat pox and lumpy skin disease virus isolates. Despite the presence of nine vaccine strains, no genetic determinants of virulence were identified on the GPCR gene. For sheep poxviruses, the addition or deletion of 21 nucleic acids (7 aa) was consistently observed in the 5′ terminal part of the gene. Specific signatures for each cluster were also identified. Prediction of the capripoxvirus GPCR topology, and its comparison with other known mammalian GPCRs and viral homologues, revealed not only a classical GPCR profile in the last three-quarters of the protein but also unique features such as a longer N-terminal end with a proximal hydrophobic α-helix and a shorter serine-rich C-tail.

scholarly journals Molecular detection and phylogenetic analysis of Lumpy skin disease virus from outbreaks in Uganda 2017-2018

2020 ◽  
Author(s):  
Sylvester Ochwo ◽  
Kimberly VanderWaal ◽  
Christian Ndekezi ◽  
Joseph Nkamwesiga ◽  
Anna Munsey ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Disease Virus ◽  
Skin Disease ◽  
Phylogenetic Trees ◽  
African Countries ◽  
Economic Implications ◽  
Lumpy Skin Disease ◽  
Lumpy Skin Disease Virus ◽  
Gpcr Gene ◽  
The Government

Abstract Background Lumpy skin disease (LSD) is an infectious viral disease of cattle caused by a capripox virus. 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 acid. 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 12bp 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 countries. Comparison of GPCR gene showed that vaccine strains were not responsible for outbreaks. This means that vaccination with the currently used vaccine will probably be effective for the control of LSD in Uganda. This information is necessary to understand LSDV molecular epidemiology and to contribute knowledge towards the development of more appropriate control strategies by the Government of Uganda.

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