Molecular characterization of serotype O foot-andmouth disease virus from pigs: Implications for multispecies approach to disease control in Uganda

In Uganda, where foot-and-mouth disease (FMD) control is mainly done through vaccination, constant monitoring of outbreaks and phylogenetic studies are important in designing effective disease control strategies. These efforts however, have mainly concentrated on cattle since they are the main visible disease hosts. In this study, the molecular characteristics of the VP1 coding sequences of the pigderived FMD virus and its phylogenetic relationship with other historical Ugandan FMD virus sequences are determined. Sixty seven samples were collected from three districts of south western Uganda and subjected to RT-PCR. Partial VP1 capsid protein coding sequences of 12 positive samples were amplified and sequenced using serotype specific primers. Eight sequences were successfully obtained, all of which were from domestic pigs. All samples were confirmed as belonging to serotype O using BLAST search. Phylogenetic analysis of the test sequences with selected sequences, showed a close relatedness (average of 3.77% pair-wise distance) to viruses isolated from central and western Uganda in the years 2005 and 2006 from cattle. These results show that domestic pigs in the western region of Uganda have been infected with the same circulating strain of FMDV and play a potentially important role in FMD maintenance and spread.Keywords: Foot-and-mouth disease (FMD), pig-derived FMDV sequence, persistence, domestic pigsAfrican Journal of Biotechnology Vol. 12(19), pp. 2547-255

Genome sequences of five African swine fever virus genotype IX isolates from domestic pigs in Uganda

Complete genome sequences of five African swine fever virus isolates were determined directly from clinical material obtained from domestic pigs in Uganda. Four sequences were essentially identical to each other, and all were closely related to the only known genome sequence of p72 genotype IX

Genome sequences of five African swine fever virus genotype IX isolates from domestic pigs in Uganda

Complete genome sequences of five African swine fever virus isolates were determined directly from clinical material obtained from domestic pigs in Uganda. Four sequences were essentially identical to each other, and all were closely related to the only known genome sequence of p72 genotype IX

Laboratory capacity for diagnosis of foot-and-mouth disease in Eastern Africa: implications for the progressive control pathway

<p>Abstract</p> <p>Background</p> <p>Accurate diagnosis is pertinent to any disease control programme. If Eastern Africa is to work towards control of foot-and-mouth disease (FMD) using the Progressive Control Pathway for FMD (PCP-FMD) as a tool, then the capacity of national reference laboratories (NRLs) mandated to diagnose FMD should match this task. This study assessed the laboratory capacity of 14 NRLs of the Eastern Africa Region Laboratory Network member countries using a semi-structured questionnaire and retrospective data from the World Reference Laboratory for FMD annual reports and Genbank® through National Centre for Biotechnology Information for the period 2006–2010.</p> <p>Results</p> <p>The questionnaire response rate was 13/14 (93%). Twelve out of the 13 countries/regions had experienced at least one outbreak in the relevant five year period. Only two countries (Ethiopia and Kenya) had laboratories at biosecurity level 3 and only three (Ethiopia, Kenya and Sudan) had identified FMD virus serotypes for all reported outbreaks. Based on their own country/region assessment, 12/13 of these countries /regions were below stage 3 of the PCP-FMD. Quarantine (77%) and vaccination (54%) were the major FMD control strategies employed. The majority (12/13) of the NRLs used serological techniques to diagnose FMD, seven used antigen ELISA and three of these (25%) also used molecular techniques which were the tests most frequently requested from collaborating laboratories by the majority (69%) of the NRLs. Only 4/13 (31%) participated in proficiency testing for FMD. Four (31%) laboratories had no quality management systems (QMS) in place and where QMS existed it was still deficient, thus, none of the laboratories had achieved accreditation for FMD diagnosis.</p> <p>Conclusions</p> <p>This study indicates that FMD diagnostic capacity in Eastern Africa is still inadequate and largely depends on antigen and antibody ELISAs techniques undertaken by the NRLs. Hence, for the region to progress on the PCP-FMD, there is need to: implement regional control measures, improve the serological diagnostic test performance and laboratory capacity of the NRLs (including training of personnel as well as upgrading of equipment and methods, especially strengthening the molecular diagnostic capacity), and to establish a regional reference laboratory to enforce QMS and characterization of FMD virus containing samples.</p

Evolutionary analysis of foot-and-mouth disease virus serotype SAT 1 isolates from east africa suggests two independent introductions from southern africa

<p>Abstract</p> <p>Background</p> <p>In East Africa, foot-and-mouth disease virus serotype SAT 1 is responsible for occasional severe outbreaks in livestock and is known to be maintained within the buffalo populations. Little is known about the evolutionary forces underlying its epidemiology in the region. To enhance our appreciation of the epidemiological status of serotype SAT 1 virus in the region, we inferred its evolutionary and phylogeographic history by means of genealogy-based coalescent methods using 53 VP1 coding sequences covering a sampling period from 1948-2007.</p> <p>Results</p> <p>The VP1 coding sequence of 11 serotype SAT 1 FMD viruses from East Africa has been determined and compared with known sequences derived from other SAT 1 viruses from sub-Saharan Africa. Purifying (negative) selection and low substitution rates characterized the SAT 1 virus isolates in East Africa. Two virus groups with probable independent introductions from southern Africa were identified from a maximum clade credibility tree. One group was exclusive to Uganda while the other was present within Kenya and Tanzania.</p> <p>Conclusions</p> <p>Our results provide a baseline characterization of the inter-regional spread of SAT 1 in sub-Saharan Africa and highlight the importance of a regional approach to trans-boundary animal disease control in order to monitor circulating strains and apply appropriate vaccines.</p

Characterisation of recent foot-and-mouth disease viruses from African buffalo ( <i>Syncerus caffer</i> ) and cattle in Kenya is consistent with independent virus populations

BACKGROUND: Understanding the epidemiology of foot-and-mouth disease (FMD), including roles played by different hosts, is essential for improving disease control. The African buffalo (Syncerus caffer) is a reservoir for the SAT serotypes of FMD virus (FMDV). Large buffalo populations commonly intermingle with livestock in Kenya, yet earlier studies have focused on FMD in the domestic livestock, hence the contribution of buffalo to disease in livestock is largely unknown. This study analysed 47 epithelia collected from FMD outbreaks in Kenyan cattle between 2008 and 2012, and 102 probang and serum samples collected from buffalo in three different Kenyan ecosystems; Maasai-Mara (MME) (n = 40), Tsavo (TSE) (n = 33), and Meru (ME) (n = 29). RESULTS: Antibodies against FMDV non-structural proteins were found in 65 of 102 (64%) sera from buffalo with 44/102 and 53/102 also having neutralising antibodies directed against FMDV SAT 1 and SAT 2, respectively. FMDV RNA was detected in 42% of the buffalo probang samples by RT-qPCR (Cycle Threshold (Ct) ≤32). Two buffalo probang samples were positive by VI and were identified as FMDV SAT 1 and SAT 2 by Ag-ELISA, while the latter assay detected serotypes O (1), A (20), SAT 1 (7) and SAT 2 (19) in the 47 cattle epithelia. VP1 coding sequences were generated for two buffalo and 21 cattle samples. Phylogenetic analyses revealed SAT 1 and SAT 2 virus lineages within buffalo that were distinct from those detected in cattle. CONCLUSIONS: We found that FMDV serotypes O, A, SAT 1 and SAT 2 were circulating among cattle in Kenya and cause disease, but only SAT 1 and SAT 2 viruses were successfully isolated from clinically normal buffalo. The buffalo isolates were genetically distinct from isolates obtained from cattle. Control efforts should focus primarily on reducing FMDV circulation among livestock and limiting interaction with buffalo. Comprehensive studies incorporating additional buffalo viruses are recommended. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12917-015-0333-9) contains supplementary material, which is available to authorized users

Genetic diversity of serotype A foot-and-mouth disease viruses in Kenya from 1964 to 2013; implications for control strategies in eastern Africa

Serotype A is the most genetically and antigenically diverse of the foot-and-mouth disease virus (FMDV) serotypes. Records of its occurrence in Kenya date back to 1952 and the antigenic diversity of the outbreak viruses in this region is reflected by the current use of two different vaccine strains (K5/1980 and K35/1980) and previous use of two other strains (K18/66 and K179/71). This study aimed at enhancing the understanding of the patterns of genetic variation of serotype A FMDV in Kenya. The complete VP1 coding region sequences of 38 field isolates, identified as serotype A FMDV, collected between 1964 and 2013 were determined. Coalescent-based methods were used to infer times of divergence of the virus strains and the evolutionary rates alongside 27 other serotype A FMDV sequences from Genbank and the World Reference Laboratory (WRL). This study represents the first comprehensive genetic analysis of serotype A FMDVs from Kenya. The study detected four previously defined genotypes/clusters (termed G-I, G-III, G-VII and G-VIII), within the Africa topotype, together with a fifth lineage that has apparently emerged from within G-I; these different lineages have each had a countrywide distribution. Genotypes G-III and G-VIII that were first isolated in 1964 are now apparently extinct; G-VII was last recorded in 2005, while G-I (including the new lineage) is currently in widespread circulation. High genetic diversity, widespread distribution and transboundary spread of serotype A FMDVs across the region of eastern Africa was apparent. Continuous surveillance for the virus, coupled to genetic and antigenic characterization is recommended for improved regional control strategies.Danish International Development Agency (DANIDA); Livestock-Wildlife Diseases in East Africa Project (LWDEA); Trans-boundary Animal Diseases in East Africa (TADEA) project: (DFC no. 10-006KU)

Unrecognized circulation of SAT 1 foot-and-mouth disease virus in cattle herds around Queen Elizabeth National Park in Uganda

BACKGROUND: Foot-and-mouth disease (FMD) is endemic in Uganda in spite of the control measures used. Various aspects of the maintenance and circulation of FMD viruses (FMDV) in Uganda are not well understood; these include the role of the African buffalo (Syncerus caffer) as a reservoir for FMDV. To better understand the epidemiology of FMD at the livestock-wildlife-interface, samples were collected from young, unvaccinated cattle from 24 pastoral herds that closely interact with wildlife around Queen Elizabeth National Park in Uganda, and analysed for evidence of FMDV infection. RESULTS: In total, 37 (15 %) of 247 serum samples had detectable antibodies against FMDV non-structural proteins (NSPs) using a pan-serotypic assay. Within these 37 sera, antibody titres ≥ 80 against the structural proteins of serotypes O, SAT 1, SAT 2 and SAT 3 were detected by ELISA in 5, 7, 4 and 3 samples, respectively, while neutralizing antibodies were only detected against serotype O in 3 samples. Two FMDV isolates, with identical VP1 coding sequences, were obtained from probang samples from clinically healthy calves from the same herd and are serotype SAT 1 (topotype IV (EA-I)). Based on the VP1 coding sequences, these viruses are distinct from previous cattle and buffalo SAT 1 FMDV isolates obtained from the same area (19–30 % nucleotide difference) and from the vaccine strain (TAN/155/71) used within Uganda (26 % nucleotide difference). Eight herds had only one or a few animals with antibodies against FMDV NSPs while six herds had more substantial evidence of prior infection with FMDV. There was no evidence for exposure to FMDV in the other ten herds. CONCLUSIONS: The two identical SAT 1 FMDV VP1 sequences are distinct from former buffalo and cattle isolates from the same area, thus, transmission between buffalo and cattle was not demonstrated. These new SAT 1 FMDV isolates differed significantly from the vaccine strain used to control Ugandan FMD outbreaks, indicating a need for vaccine matching studies. Only six herds had clear serological evidence for exposure to O and SAT 1 FMDV. Scattered presence of antibodies against FMDV in other herds may be due to the occasional introduction of animals to the area or maternal antibodies from past infection and/or vaccination. The evidence for asymptomatic FMDV infection has implications for disease control strategies in the area since this obstructs early disease detection that is based on clinical signs in FMDV infected animals. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12917-015-0616-1) contains supplementary material, which is available to authorized users

Time clustered sampling can inflate the inferred substitution rate in foot-and-mouth disease virus analyses

With the emergence of analytical software for the inference of viral evolution, a number of studies have focused on estimating important parameters such as the substitution rate and the time to the most recent common ancestor (tMRCA) for rapidly evolving viruses. Coupled with an increasing abundance of sequence data sampled under widely different schemes, an effort to keep results consistent and comparable is needed. This study emphasizes commonly disregarded problems in the inference of evolutionary rates in viral sequence data when sampling is unevenly distributed on a temporal scale through a study of the foot-and-mouth (FMD) disease virus serotypes SAT 1 and SAT 2. Our study shows that clustered temporal sampling in phylogenetic analyses of FMD viruses will strongly bias the inferences of substitution rates and tMRCA because the inferred rates in such data sets reflect a rate closer to the mutation rate rather than the substitution rate. Estimating evolutionary parameters from viral sequences should be performed with due consideration of the differences in short-term and longer-term evolutionary processes occurring within sets of temporally sampled viruses, and studies should carefully consider how samples are combined

High Levels of Genetic Differentiation between Ugandan Glossina fuscipes fuscipes Populations Separated by Lake Kyoga

The two types of sleeping sickness in West and East Africa are markedly distinct, require different treatments, and are caused by different parasites. The only country where both parasites are present is Uganda, where they are separated by a narrow 160 km disease-free belt. Because there is no restriction on the movement of humans and animals between the two disease zones, this separation is puzzling. We asked whether this disjunct distribution can be explained by variation within the tsetse fly that is largely responsible for transmitting both diseases in Uganda, Glossina fuscipes fuscipes. We therefore examined whether this tsetse subspecies is genetically uniform across Uganda. Our results indicate that G. f. fusicipes is not genetically different between the two disease zones, but there are clear genetic differences between northern and southern populations, which are separated by Lake Kyoga. Therefore, it is unlikely that variation in the tsetse fly determines the distribution of the two parasites. This implies that the two diseases may fuse in the near future, which would greatly complicate diagnosis and treatment of sleeping sickness in any potential area of overlap