Table 4 Assessment of epidemiological and genomic evidence for transmission among animals from experiment G and from the field outbreak
Samples | Description of contact | Consensus-level and within-sample diversity | Probability of transmission inferred from within-sample diversity |
|---|---|---|---|
Experiment G: G_2035, G_7971, G_2073, G_2078, G_7992 | Experimental transmission from G_2035 to G_7971 and from G_7971 to G_2073, G_2078 and G_7992 | No consensus-level diversity | No transmission link inferred with high confidence (max. probability 35%) |
Field outbreak: BE11J20, BK11J20 | Day 0: One cattle, which did not develop clinical signs, moved from BE to BK Day 2: BRSV diagnosed in BE Day 11: BRSV diagnosed in BK | One change T → C (synonymous) at position 9640, in gene L, unique to BK11J20. BK11J20 is the only field sample with > 1% diversity at this site (13 × C, 2 × T) | BE11J20 → BK11J20: 68% |
Field outbreak: AI12U20, AI14U20, AJ11U20, AJ22U20, AL11U20 | Day 0: AL received calves from AJ Day 11: Animal professional visited both herds Day 20 and 21: AI and AJ received visit from same organisation, respectively, for the same purpose, possibly same material. AI and AJ are geographically close (500–1000 m) Day 33: BRSV diagnosed in AI Day 34: BRSV diagnosed in AJ Day 36: BRSV diagnosed in AL | One change A → G (non-synonymous Ile → Met) at position 3981, in gene M, unique to AJ22U20. AJ22U20 is the only field sample with diversity > 1% at this site (319 × A, 409 × G). All other AI, AJ and AL consensus sequences were identical | Between herd No transmission links inferred with high confidence (max. probability 53%) Within herd AI12U20 → AI14U20: 53% AJ22U20 → AJ11U20: 51% |