We performed a phylogenetic analysis of caprine and ovine lentiviruses using long sequences in gag and pol of 104 new Swiss isolates and six available corresponding database sequences. Forty-five isolates, forming five sequence clusters, were unclassifiable by the present classification. Pairwise DNA distance analysis indicated different categories of relatedness, requiring a new classification system. We propose four principal sequence groups, A-D, which differ by 25-37%. Groups A and B are further divided into subtypes which differ by 15-27%. Group D and four of the seven group A subtypes, A3, A4, A5 and A7, are formed by new Swiss isolates. Molecular epidemiology revealed that Swiss B1 strains differed no more from French, Brazilian or US strains than from each other, suggesting virus propagation through international livestock trade. Furthermore, infection of goats by subtypes A3 or A4 was significantly associated with documented contact with sheep, which also harbor these subtypes, thus indicating regularly occurring sheep-to-goat transmission.

Equine influenza virus (EIV) surveillance is important in the management of equine influenza. It provides data on circulating and newly emerging strains for vaccine strain selection. To this end, antigenic characterisation by haemaggluttination inhibition (HI) assay and phylogenetic analysis was carried out on 28 EIV strains isolated in North America and Europe during 2006 and 2007. In the UK, 20 viruses were isolated from 28 nasopharyngeal swabs that tested positive by enzyme-linked immunosorbent assay. All except two of the UK viruses were characterised as members of the Florida sublineage with similarity to A/eq/Newmarket/5/03 (clade 2). One isolate, A/eq/Cheshire/1/06, was characterised as an American lineage strain similar to viruses isolated up to 10 years earlier. A second isolate, A/eq/Lincolnshire/1/07 was characterised as a member of the Florida sublineage (clade 1) with similarity to A/eq/Wisconsin/03. Furthermore, A/eq/Lincolnshire/1/06 was a member of the Florida sublineage (clade 2) by haemagglutinin (HA) gene sequence, but appeared to be a member of the Eurasian lineage by the non-structural gene (NS) sequence suggesting that reassortment had occurred. A/eq/Switzerland/P112/07 was characterised as a member of the Eurasian lineage, the first time since 2005 that isolation of a virus from this lineage has been reported. Seven viruses from North America were classified as members of the Florida sublineage (clade 1), similar to A/eq/Wisconsin/03. In conclusion, a variety of antigenically distinct EIVs continue to circulate worldwide. Florida sublineage clade 1 viruses appear to predominate in North America, clade 2 viruses in Europe.

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The prevalences of Cryptosporidium parvum, rotavirus, bovine coronavirus (BCV), and enterotoxigenic Escherichia coli (E coli K99) were determined in diarrhoeic dairy calves aged one to 21 days on 71 dairy farms in western Switzerland during the winter of 2005 to 2006. Faecal samples from 147 untreated calves suffering from acute diarrhoea were analysed by standardised diagnostic methods, and the immunoglobulin status of each calf was evaluated. The prevalences of C parvum, rotavirus, BCV and E coli k99 were 55.0 per cent, 58.7 per cent, 7.8 per cent and 5.5 per cent, respectively. The proportions of herds positive for the respective pathogens among the herds with diarrhoeic calves were 41.7 per cent, 52.1 per cent, 2.1 per cent and 2.1 per cent. The immunoglobulin concentration in the serum of 90.5 per cent of the diarrhoeic calves was below 8 g/l.

Based on available sequence data, a phylogeny of small ruminant lentiviruses (SRLV) was established for env, pol, gag and LTR fragments using maximum likelihood, neighbour-joining and minimum evolution reconstruction techniques. To reconstruct topologies as accurately as possible, phylogenetic parameters like base composition, percentage divergences, kappa, the gamma shape parameter alpha and codon position-specific rates were estimated prior to the reconstruction of trees. Divergences between fragments of SRLV ranged from 16 % in gag and pol to 22 % in env and 35 % in LTR. The codon position bias found and the ratios of synonymous to nonsynonymous substitutions were inversely related to overall divergence, indicating the existence of both negative and positive Dar-