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Complete genome sequences were determined for two distinct strains of slow bee paralysis virus (SBPV) of honeybees (Apis mellifera). The SBPV genome is approximately 9.5 kb long and contains a single ORF flanked by 59-and 39-UTRs and a naturally polyadenylated 39 tail, with a genome organization typical of members of the family Iflaviridae. The two strains, labelled 'Rothamsted' and 'Harpenden', are 83 % identical at the nucleotide level (94 % identical at the amino acid level), although this variation is distributed unevenly over the genome. The two strains were found to co-exist at different proportions in two independently propagated SBPV preparations. The natural prevalence of SBPV for 847 colonies in 162 apiaries across five European countries was ,2 %, with positive samples found only in England and Switzerland, in colonies with variable degrees of Varroa infestation.Slow bee paralysis virus (SBPV) is one of several honeybee (Apis mellifera) viruses linked to high mortality of colonies infested with the ectoparasitic mite Varroa destructor (Carreck et al., 2010;Martin et al., 1998). SBPV was discovered fortuitously in England in 1974, during propagation experiments involving bee virus X. It induces paralysis of the anterior two pairs of legs about 10 days after injection into the abdomen of adult bees (Bailey & Woods, 1974), with high virus accumulation in the head, the hypopharyngeal, mandibular and salivary glands, the fat body, crop and forelegs, but less in the hindlegs, midgut, rectum and thorax (Denholm, 1999). Like most honeybee viruses, SBPV persists naturally as a covert infection, most likely through oral transmission (Bailey & Ball, 1991). However, SBPV can be transmitted readily among adult bees and to pupae by Varroa mites (Santillán-Galicia et al., 2010), with lethal consequences at the individual bee and colony levels (Carreck et al., 2010). Overt SBPV infection can also be induced in adult bees (but not in pupae) by injection with inert fluids, especially the The GenBank/EMBL/DDBJ accession numbers for the complete genome sequences of SBPV strains Rothamsted and Harpenden are EU035616 and GU938761, respectively.A supplementary table showing primers and performance indicators of several universal and strain-specific RT-qPCR assays is available with the online version of this paper.

BackgroundAvian pathogenic Escherichia coli (APEC) causes colibacillosis, which results in significant economic losses to the poultry industry worldwide. However, the diversity between isolates remains poorly understood. Here, a total of 272 APEC isolates collected from the United Kingdom (UK), Italy and Germany were characterised using multiplex polymerase chain reactions (PCRs) targeting 22 equally weighted factors covering virulence genes, R-type and phylogroup. Following these analysis, 95 of the selected strains were further analysed using Whole Genome Sequencing (WGS).ResultsThe most prevalent phylogroups were B2 (47%) and A1 (22%), although there were national differences with Germany presenting group B2 (35.3%), Italy presenting group A1 (53.3%) and UK presenting group B2 (56.1%) as the most prevalent. R-type R1 was the most frequent type (55%) among APEC, but multiple R-types were also frequent (26.8%). Following compilation of all the PCR data which covered a total of 15 virulence genes, it was possible to build a similarity tree using each PCR result unweighted to produce 9 distinct groups. The average number of virulence genes was 6–8 per isolate, but no positive association was found between phylogroup and number or type of virulence genes. A total of 95 isolates representing each of these 9 groupings were genome sequenced and analysed for in silico serotype, Multilocus Sequence Typing (MLST), and antimicrobial resistance (AMR). The UK isolates showed the greatest variability in terms of serotype and MLST compared with German and Italian isolates, whereas the lowest prevalence of AMR was found for German isolates. Similarity trees were compiled using sequencing data and notably single nucleotide polymorphism data generated ten distinct geno-groups. The frequency of geno-groups across Europe comprised 26.3% belonging to Group 8 representing serogroups O2, O4, O18 and MLST types ST95, ST140, ST141, ST428, ST1618 and others, 18.9% belonging to Group 1 (serogroups O78 and MLST types ST23, ST2230), 15.8% belonging to Group 10 (serogroups O8, O45, O91, O125ab and variable MLST types), 14.7% belonging to Group 7 (serogroups O4, O24, O35, O53, O161 and MLST type ST117) and 13.7% belonging to Group 9 (serogroups O1, O16, O181 and others and MLST types ST10, ST48 and others). The other groups (2, 3, 4, 5 and 6) each contained relatively few strains.However, for some of the genogroups (e.g. groups 6 and 7) partial overlap with SNPs grouping and PCR grouping (matching PCR groups 8 (13 isolates on 22) and 1 (14 isolates on 16) were observable). However, it was not possible to obtain a clear correlation between genogroups and unweighted PCR groupings. This may be due to the genome plasticity of E. coli that enables strains to carry the same virulence factors even if the overall genotype is substantially different.ConclusionsThe conclusion to be drawn from the lack of correlations is that firstly, APEC are very diverse and secondly, it is not possible to rely on any one or more basic molecular or phenotypic tests t...

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