VP1 sequencing protocol for foot and mouth disease virus molecular epidemiology.

Nucleotide sequences of field strains of foot and mouth disease virus (FMDV) contribute to our understanding of the distribution and evolution of viral lineages that circulate in different regions of the world. This paper outlines a practical reversetranscription polymerase chain reaction (RT-PCR) and sequencing strategy that can be used to generate RNA sequences encoding the VP1 (1D) region of FMDV. The protocol contains a panel of PCR and sequencing primers that can be selected to characterise genetically diverse isolates representing all seven FMDV serotypes. A list of sequences is also described, comprising prototype sequences for all proposed FMDV topotypes, in order to provide a framework for phylogenetic analysis. The technical details and prototype sequences provided in this paper can be employed by FMD Reference Laboratories and others in an approach to harmonise the molecular epidemiology of FMDV.

Les séquences de nucléotides des souches de terrain du virus de la fièvre aphteuse nous aident à comprendre la distribution et l'évolution des lignées virales présentes dans les différentes régions du monde. Les auteurs décrivent les grandes lignes d'un protocole pratique, basé sur l'amplification en chaîne par polymérase couplée à une transcription inverse (RT-PCR) et sur le séquençage, qui peut être utilisé pour générer des séquences d'ARN codant pour la région VP1 (1D) du virus de la fièvre aphteuse. Le protocole permet de procéder à une sélection parmi un panel de PCR et de marqueurs de séquençage dans le but de caractériser les gènes de divers isolats représentant les sept sérotypes du virus de la fièvre aphteuse. Les auteurs décrivent également une liste de séquences pouvant servir de cadre à l'analyse phylogénétique, dont des séquences prototypes pour tous les topotypes proposés du virus de la fièvre aphteuse. Les données techniques détaillées et les séquences prototypes fournies par les auteurs peuvent être utilisées par les Laboratoires de référence pour la fièvre aphteuse et d'autres institutions, en vue d'harmoniser l'épidémiologie moléculaire du virus de la fièvre aphteuse.

Las secuencias nucleotídicas de las cepas salvajes del virus de la fiebre aftosa nos ayudan a entender la distribución y evolución de los linajes víricos circulantes en distintas regiones del mundo. Los autores exponen sucintamente un práctico procedimiento de reacción en cadena de la polimerasa acoplada a transcripción inversa (RT-PCR) y de secuenciación que se puede utilizar para generar secuencias de ARN que codifican la región VP1 (1D) del virus de la fiebre aftosa. El protocolo ofrece la posibilidad de elegir entre todo un repertorio de cebadores de PCR y de secuenciación en el que están representados los siete serotipos víricos existentes con objeto de caracterizar genéticamente diversas cepas aisladas sobre el terreno. Los autores también presentan una lista de secuencias que comprende secuencias prototípicas de todos los topotipos propuestos del virus, a fin de proporcionar un marco de referencia para el análisis filogenético. Los laboratorios de referencia para la fiebre aftosa, así como otros establecimientos, pueden servirse de las detalladas técnicas y las secuencias prototípicas aquí presentadas para armonizar el estudio de la epidemiología molecular del virus de la fiebre aftosa.

African horse sickness in The Gambia: circulation of a live-attenuated vaccine-derived strain.

African horse sickness virus serotype 9 (AHSV-9) has been known for some time to be circulating amongst equids in West Africa without causing any clinical disease in indigenous horse populations. Whether this is due to local breeds of horses being resistant to disease or whether the AHSV-9 strains circulating are avirulent is currently unknown. This study shows that the majority (96%) of horses and donkeys sampled across The Gambia were seropositive for AHS, despite most being unvaccinated and having no previous history of showing clinical signs of AHS. Most young horses (<3 years) were seropositive with neutralizing antibodies specific to AHSV-9. Eight young equids (<3 years) were positive for AHSV-9 by serotype-specific RT-PCR and live AHSV-9 was isolated from two of these horses. Sequence analysis revealed the presence of an AHSV-9 strain showing 100% identity to Seg-2 of the AHSV-9 reference strain, indicating that the virus circulating in The Gambia was highly likely to have been derived from a live-attenuated AHSV-9 vaccine strain.

Bluetongue virus: European Community proficiency test (2007) to evaluate ELISA and RT-PCR detection methods with special reference to pooling of samples.

Bluetongue virus European Community national reference laboratories (BTV-EC-NRLs) participated in an inter-laboratory proficiency test in 2007. The aim of the inter-laboratory proficiency test was to determine the ability of laboratories to detect antibodies to a series of BTV serotypes by cELISA and to detect viral RNA in animals infected with the European strain of BTV-8 by RT-PCR. Both serum and EDTA blood sample were diluted in order to determine the sensitivity of the assays. All the cELISAs were 'fit-for purpose' to detect antibodies to the common BTV serotypes circulating in Europe and the real time RT-PCR assays were all capable of detecting BTV-8 RNA albeit with varying sensitivities. There were however inconsistencies in the ability of the gel-based PCR assays to detect BTV RNA. In addition, samples taken on the first day of viraemia and at the peak of viraemia from animals experimentally infected with BTV-8, were diluted to determine if the diluting of samples affected the ability of the Shaw et al. (Shaw, A.E., M., P., Alpar, H.O., Anthony, S., Darpel, K.E., Batten, C.A., Carpenter, S., Jones, H., Oura, C.A.L., King, D.P., Elliott, H., Mellor, P.S., Mertens, P.P.C., 2007. Development and validation of a real-time RT-PCR assay to detect genome bluetongue virus segment 1. Journal of Virological Methods) RT-PCR assay to detect BTV-RNA at these time-points. Results indicated that, if samples were taken at the onset of viraemia, diluting at 1/5 resulted in a reduced ability of the assay to detect BTV RNA in the diluted compared to the neat samples. Diluting samples taken at the peak of viraemia at 1/10 however resulted in no loss in sensitivity.

The evolution and phylodynamics of serotype A and SAT2 foot-and-mouth disease viruses in endemic regions of Africa.

Foot-and-mouth disease (FMD) is a major livestock disease with direct clinical impacts as well as indirect trade implications. Control through vaccination and stamping-out has successfully reduced or eradicated the disease from Europe and large parts of South America. However, sub-Saharan Africa remains endemically affected with 5/7 serotypes currently known to be circulating across the continent. This has significant implications both locally for livestock production and poverty reduction but also globally as it represents a major reservoir of viruses, which could spark new epidemics in disease free countries or vaccination zones. This paper describes the phylodynamics of serotypes A and SAT2 in Africa including recent isolates from Cameroon in Central Africa. We estimated the most recent common ancestor for serotype A was an East African virus from the 1930s (median 1937; HPD 1922-1950) compared to SAT2 which has a much older common ancestor from the early 1700s (median 1709; HPD 1502-1814). Detailed analysis of the different clades shows clearly that different clades are evolving and diffusing across the landscape at different rates with both serotypes having a particularly recent clade that is evolving and spreading more rapidly than other clades within their serotype. However, the lack of detailed sequence data available for Africa seriously limits our understanding of FMD epidemiology across the continent. A comprehensive view of the evolutionary history and dynamics of FMD viruses is essential to understand many basic epidemiological aspects of FMD in Africa such as the scale of persistence and the role of wildlife and thus the opportunities and scale at which vaccination and other controls could be applied. Finally we ask endemic countries to join the OIE/FAO supported regional networks and take advantage of new cheap technologies being rolled out to collect isolates and submit them to the World Reference Laboratory.

Bluetongue virus: European Community inter-laboratory comparison tests to evaluate ELISA and RT-PCR detection methods.

European Community national reference laboratories participated in two inter-laboratory comparison tests in 2006 to evaluate the sensitivity and specificity of their 'in-house' ELISA and RT-PCR assays for the detection of bluetongue virus (BTV) antibodies and RNA. The first ring trial determined the ability of laboratories to detect antibodies to all 24 serotypes of BTV. The second ring trial, which included both antisera and EDTA blood samples from animals experimentally infected with the northern European strain of BTV-8, determined the ability of laboratories to detect BTV-8 antibodies and RNA, as well as the diagnostic sensitivity of the assays. A total of six C-ELISAs, six real-time RT-PCR and three conventional RT-PCR assays were used. All C-ELISAs were capable of detecting the BTV serotypes currently circulating in Europe (BTV-1, 2, 4, 8, 9 and 16), however some assays displayed inconsistencies in the detection of other serotypes, particularly BTV-19. All C-ELISAs detected BTV-8 antibodies in cattle and sheep by 21 dpi, while the majority of assays detected antibodies by 9 dpi in cattle and 8 dpi in sheep. All the RT-PCR assays were able to detect BTV-8, although the real-time assays were more sensitive compared to the conventional assays. The majority of real-time RT-PCR assays detected BTV RNA as early as 2 dpi in cattle and 3 dpi in sheep. These two ring trails provide evidence that national reference laboratories within the EC are capable of detecting BTV antibodies and RNA and provide specificity and sensitivity information on the detection methods currently available.

Clinical signs and pathology shown by British sheep and cattle infected with bluetongue virus serotype 8 derived from the 2006 outbreak in northern Europe.

Four poll Dorset sheep and four Holstein-Friesian cattle were infected with the northern European strain of bluetongue virus (BTV), BTV-8, to assess its pathogenicity in UK breeds. The time course of infection was monitored in both species by using real-time reverse transcriptase-PCR (RT-PCR), conventional RT-PCR and serology. Two of the sheep developed severe clinical signs that would have been fatal in the field; the other two were moderately and mildly ill, respectively. The cattle were clinically unaffected, but had high levels of viral RNA in their bloodstream. Real-time RT-PCR detected viral RNA as early as one day after infection in the cattle and three days after infection in the sheep. Antibodies against BTV were detected by six days after infection in the sheep and eight days after infection in the cattle. Postmortem examinations revealed pathology in the cattle that was more severe than suggested by the mild clinical signs, but the pathological and clinical findings in the sheep were more consistent.

Genome Sequence of Foot-and-Mouth Disease Virus Serotype O Isolated from Morocco in 2015.

The genome of a virus isolated from an outbreak of foot-and-mouth disease (FMD) in Morocco in 2015 is described here. This virus is classified as lineage Ind-2001d within serotype O, topotype ME-SA (Middle East-South Asia). This lineage is endemic on the Indian subcontinent but has caused outbreaks in the Middle East and North Africa since 2013.

Complete Genome Sequence of a Serotype A Foot-and-Mouth Disease Virus from an Outbreak in Saudi Arabia during 2015.

The complete genome of a foot-and-mouth disease (FMD) type A virus isolated from cattle in Saudi Arabia in 2015 is described here. This virus belongs to an FMD virus lineage named genotype VII, which is normally endemic on the Indian subcontinent.

Adverse Reactions to Field Vaccination Against Lumpy Skin Disease in Jordan.

Lumpy skin disease (LSD) is an emerging disease in the Middle East region and has been recently reported in Jordan. The aim of this study was to investigate the adverse reactions that were reported after vaccine administration. Geographical areas enrolled in the study were free of the disease and away from the outbreak governorate. Sixty-three dairy cattle farms, with a total of 19,539 animals, were included in the study. Of those, 56 farms reported adverse clinical signs after vaccine administration. The duration between vaccine administration and appearance of adverse clinical signs ranged from 1 to 20 days (Mean = 10.3, SD ± 3.9). Clinical signs were similar to those observed with natural cases of lumpy skin disease. These were mainly fever, decreased feed intake, decreased milk production and variable sized cutaneous nodules (a few millimetres to around 2 cm in diameter) that could be seen anywhere on the body (head, neck, trunk, perineum), udder, and/or teats. Nodules were raised and firm initially and then formed dry scabs that could be peeled off the skin. The characteristic deep 'sit fast' appearance was rarely seen and most lesions were superficial. Some cattle had swollen lymph nodes, while a few pregnant animals aborted. The percentage of affected cattle ranged from 0.3 to 25% (Mean = 8, SD ± 5.1). Fever, decreased feed intake, and decreased milk production were seen in 83.9, 85.7, and 94.6% in cattle on the affected farms, respectively. All affected cattle displayed skin nodules over their entire bodies, while 33.9 and 7.1% of the affected farms reported nodular lesions present on the udders and teats, respectively. No mortalities were reported due to vaccine adverse reactions. Duration (course) of clinical signs ranged from 3 to 20 days (Mean = 13.7, SD ± 4.1). Two types of LSD vaccines were used by the farmers in this study. The first one was a sheep pox virus (SPPV) vaccine derived from the RM65 isolate [Jovivac, manufactured by Jordan Bioindustries Centre (JOVAC)] and the other an unlabelled one, which was later identified using PCR as a strain of lumpy skin disease virus (LSDV). Blood and skin samples collected from cattle vaccinated with the LSDV vaccine were positive for LSDV using both general and species-specific PCR primers, whereas those from cattle vaccinated with the Jovivac vaccine were negative. Adverse reactions observed in cattle after administration of the LSDV vaccine were reported to be more severe than those seen after Jovivac vaccine administration and were comparable with clinical signs observed in natural infections.

Outbreaks of Foot-and-Mouth Disease in Libya and Saudi Arabia During 2013 Due to an Exotic O/ME-SA/Ind-2001 Lineage Virus.

Foot-and-mouth disease viruses are often restricted to specific geographical regions and spread to new areas may lead to significant epidemics. Phylogenetic analysis of sequences of the VP1 genome region of recent outbreak viruses from Libya and Saudi Arabia has revealed a lineage, O-Ind-2001, normally found in the Indian subcontinent. This paper describes the characterization of field viruses collected from these cases and provides information about a new real-time RT-PCR assay that can be used to detect viruses from this lineage and discriminate them from other endemic FMD viruses that are co-circulating in North Africa and western Eurasia.

African horse sickness outbreaks caused by multiple virus types in Ethiopia.

African horse sickness (AHS) is associated with high morbidity and mortality in equids, especially horses. A retrospective analysis was carried out concerning 737 AHS outbreaks that occurred during 2007-2010 in Ethiopia. A total of ten outbreaks were investigated in the study period. All four forms of the disease (pulmonary, cardiac, horse sickness fever and the combined form) were observed, with the cardiac form being the most prevalent. Multiple African horse sickness virus serotypes (AHSV-2, AHSV-4, AHSV-6, AHSV-8 and AHSV-9) were detected by molecular methods (type-specific real-time RT-PCR assays), and fourteen isolates were derived from blood and tissue samples collected during 2009-2010. This is the first report of AHSV-4, AHSV-6 or AHSV-8 in Ethiopia.

Genetic and phylogenetic analysis of the outer-coat proteins VP2 and VP5 of epizootic haemorrhagic disease virus (EHDV): comparison of genetic and serological data to characterise the EHDV serogroup.

The outer-coat proteins, VP2 and VP5, of epizootic haemorrhagic disease virus (EHDV) are important for host cell binding during the initiation of infection. They are also known to determine virus serotype. This study presents a complete genetic and phylogenetic analysis of these proteins (and the genes that code for them) to allow comparison of the selective pressures acting on each and the correlation of genetic sequence data with serotype. Accession numbers, gene and protein sizes, ORF positions, G+C contents, terminal hexanucleotides, start and stop codons and phylogenetic relationships are all presented. The results show that VP2 is highly variable, is under great pressure to adapt and can be correlated with serotype. While also variable, VP5 appears to be under less adaptive pressure than VP2 but still shows some correlation with serotype. Seven serotypes of EHDV have been defined in this study, although the results do show that some serotypes are extremely closely related--and highlight the benefit of using both molecular and serologic analyses. Analysis of the terminal hexanucleotides showed that the 5' terminus is under greater purifying selection than the 3'. Evidence is also presented that both segments 2 and 6 (coding for VP2 and VP5 respectively) have grown via gene duplication and subsequent mutation.