Table 1.
New infectious agent variants and species, their characteristics and taxonomic diversity
| All types | Virus (All) | Virus (DNA) | Virus (RNA) | Bacteria | Others | |
|---|---|---|---|---|---|---|
| New infectious agent variants | ||||||
| .New variants (%) | 173 (100%) | 74 (43%) | 17 (10%) | 57 (33%) | 93 (54%) | 6 (3%) |
| .Taxonomic diversity | ||||||
| ..Species inc. new variants (d) | 91 (1.9) | 42 (1.8) | 17 (1) | 25 (2.3) | 43 (2.2) | 6 (1) |
| ..Genera inc. new variants (d) | 63 (2.7) | 32 (2.3) | 10 (1.7) | 22 (2.6) | 26 (3.6) | 5 (1.2) |
| ..Families inc. new variants (d) | 47 (3.7) | 21 (3.5) | 6 (2.8) | 15 (3.8) | 21 (4.4) | 5 (1.2) |
| .Country group | ||||||
| ..HIC (%) | 138 (80%) | 44 (59%) | 12 (71%) | 32 (56%) | 91 (98%) | 3 (50%) |
| ..LMIC (%) | 35 (20%) | 30 (41%) | 5 (29%) | 25 (44%) | 2 (2%) | 3 (50%) |
| .Host Range | ||||||
| ..From swine-sp. species (%)a | 64 (37%) | 39 (53%) | 17 (100%) | 22 (39%) | 25 (27%) | 0 (0%) |
| …In HIC (%) | 51 (37%) | 26 (59%) | 12 (100%) | 14 (44%) | 25 (27%) | 0 (0%) |
| …In LMIC (%) | 13 (37%) | 13 (43%) | 5 (100%) | 8 (32%) | 0 (0%) | 0 (0%) |
| …RR (CI, p) | 1 (0.6-1.8, p = 1) | 1.4 (0.9-2.4, p = 0.2) | - | - | - | - |
| ..From zoonotic species (%)a | 95 (55%) | 33 (45%) | 0 (0%) | 33 (58%) | 58 (62%) | 4 (67%) |
| …In HIC (%) | 75 (54%) | 17 (39%) | 0 (0%) | 17 (53%) | 56 (62%) | 2 (67%) |
| …In LMIC (%) | 20 (57%) | 16 (53%) | 0 (0%) | 16 (64%) | 2 (100%) | 2 (67%) |
| …RR (CI, p) | 1 (0.7-1.4, p = 0.9) | 0.7 (0.4-1.2, p = 0.2) | - | - | - | - |
| .Context of detection | ||||||
| ..Outbreak investigation (n,%) | 58 (144, 40%) | 18 (68, 26%) | 2 (17, 12%) | 16 (51, 31%) | 39 (70, 56%) | 1 (6, 17%) |
| …In HIC (%) | 51 (112, 46%) | 12 (41, 29%) | 2 (12, 17%) | 10 (29, 34%) | 38 (68, 56%) | 1 (3, 33%) |
| …In LMIC (%) | 7 (32, 22%) | 6 (27, 22%) | 0 (5, 0%) | 6 (22, 27%) | 1 (2, 50%) | 0 (3, 0%) |
| …RR (CI, p) | 2.1 (1.2-5.4, p = 0.02) | 1.3 (0.6-4, p = 0.6) | - | - | - | - |
| New infectious agent species | ||||||
| .New species (%) | 73 (100%) | 35 (48%) | 17 (23%) | 18 (25%) | 32 (44%) | 6 (8%) |
| ..Unknown before disc. in pigs | 50 (68%) | 27 (37%) | 17 (23%) | 10 (14%) | 22 (30%) | 1 (1%) |
| ..Known to infect other hosts | 23 (32%) | 8 (11%) | 0 (0%) | 8 (11%) | 10 (14%) | 5 (7%) |
| .Taxonomic diversity | ||||||
| ..Genera inc. new species (d) | 52 (1.4) | 26 (1.3) | 10 (1.7) | 16 (1.1) | 21 (1.5) | 5 (1.2) |
| ..Families inc. new species (d) | 44 (1.7) | 19 (1.8) | 6 (2.8) | 13 (1.4) | 20 (1.6) | 5 (1.2) |
| .Country group | ||||||
| ..HIC (%) | 54 (74%) | 20 (57%) | 12 (71%) | 8 (44%) | 31 (97%) | 3 (50%) |
| ..LMIC (%) | 19 (26%) | 15 (43%) | 5 (29%) | 10 (56%) | 1 (3%) | 3 (50%) |
| .Host Range | ||||||
| ..From swine-sp. species (%) | 37 (51%) | 24 (69%) | 17 (100%) | 7 (39%) | 13 (41%) | 0 (0%) |
| …In HIC (%) | 30 (56%) | 17 (85%) | 12 (100) | 5 (62%) | 13 (42%) | 0 (0%) |
| …In LMIC (%) | 7 (37%) | 7 (47%) | 5 (100%) | 2 (20%) | 0 (0%) | 0 (0%) |
| …RR (CI, p) | 1.5 (0.9-3.5, p = 0.2) | 1.8 (1.1-4, p = 0.03) | - | - | - | - |
| ..From zoonotic species (%) | 24 (33%) | 9 (26%) | 0 (0%) | 9 (50%) | 11 (34%) | 4 (67%) |
| …In HIC (%) | 14 (26%) | 2 (10%) | 0 (0%) | 2 (25%) | 10 (32%) | 2 (67%) |
| …In LMIC (%) | 10 (53%) | 7 (47%) | 0 (0%) | 7 (70%) | 1 (100%) | 2 (67%) |
| …RR (CI, p) | 0.5 (0.3-1, p < 0.05) | 0.2 (0–0.7, p = 0.02) | - | - | - | - |
| .Context of detection | ||||||
| ..Outbreak investigation (n,%) | 17 (23%) | 6 (17%) | 2 (12%) | 4 (22%) | 10 (31%) | 1 (17%) |
| …In HIC (%) | 16 (30%) | 5 (25%) | 2 (17%) | 3 (38%) | 10 (32%) | 1 (33%) |
| …In LMIC (%) | 1 (5%) | 1 (7%) | 0 (0%) | 1 (10%) | 0 (0%) | 0 (0%) |
| …RR (CI, p) | 5.6 (1.5-∞, p = 0.03) | 3.8 (0.8-∞, p = 0.2) | - | - | - | - |
“Others” refer to fungi, helminths and protozoa; d: average number of new variants (or new species) per taxon; HIC high-income countries; LMIC low- and middle-income countries; RR risk ratio; p: Fisher’s exact test p-value. RRs were only computed for all data and viruses, because of the low number of variants and species in one or the two country groups for other infectious agent types.a The host range of the species to which new variants belonged was taken into account.