Table 3. Overview of samples and viruses detected at family level in the distal jejunum of neonatal piglets with and without diarrhoea.
| Sample ID | Herd | Health status | Age (Days)a | Mammalian viruses detected (No. of reads)b | Mammalian viruses detected (No. reads)c | Mammalian viruses detected (No. reads)d |
|---|---|---|---|---|---|---|
| Kraken | Diamond | HMM/vFam | ||||
| 1A | A | Healthy | 2 | Picornaviridae (57891) | Picornaviridae (27997) | Picornaviridae (25840) |
| N/A | N/A | Parvoviridae (8) | ||||
| 2A | A | Healthy | 1 | Picornaviridae (174352) | Picornaviridae (106330) | Picornaviridae (95786) |
| Caliciviridae (184) | N/A | Caliciviridae (4480) | ||||
| Parvoviridae (13) | N/A | Parvoviridae (2) | ||||
| N/A | Circoviridae (4) | Circoviridae (27) | ||||
| Pool A | A | Diarrhoeic | 1 | Reoviridae (2) | N/A | Reoviridae (1) |
| 1B | B | Healthy | 4 | Picornaviridae (1201) | N/A | Picornaviridae (750) |
| Reoviridae (28874) | Reoviridae (21161) | Reoviridae (18127) | ||||
| Circoviridae (88) | Circoviridae (85) | Circoviridae (213) | ||||
| N/A | N/A | Adenoviridae (18) | ||||
| 2B | B | Healthy | 5 | Picornaviridae (52101) | Picornaviridae (27870) | Picornaviridae (29473) |
| Reoviridae (6) | Reoviridae (6) | Reoviridae (52) | ||||
| Circoviridae (946) | Circoviridae (731) | Circoviridae (389) | ||||
| N/A | N/A | Adenoviridae (33) | ||||
| Pool B | B | Diarrhoeic | 3.2 | Picornaviridae (880) | Picornaviridae (460) | Picornaviridae (605) |
| N/A | N/A | Caliciviridae (48) | ||||
| Reoviridae (690) | Reoviridae (1184) | Reoviridae (1372) | ||||
| 1C | C | Healthy | 3 | Picornaviridae (1615) | Picornaviridae (798) | Picornaviridae (807) |
| Astroviridae (23) | Astroviridae (15) | Astroviridae (27) | ||||
| Circoviridae (10) | Circoviridae (6) | Circoviridae (53) | ||||
| N/A | N/A | Caliciviridae (42) | ||||
| 2C | C | Healthy | 1 | N/A | Circoviridae (2) | Circoviridae (45) |
| Pool C | C | Diarrhoeic | 1.9 | N/A | N/A | N/A |
| 1D | D | Healthy | 1 | Circoviridae (1) | Circoviridae (3) | Circoviridae (998) |
| Adenoviridae (1) | Adenoviridae (1) | Adenoviridae (10) | ||||
| 2D | D | Healthy | 1 | N/A | Circoviridae (19) | Circoviridae (47) |
| Pool D | D | Diarrhoeic | 1.2 | N/A | N/A | N/A |
| 1E | E | Healthy | 1 | Anelloviridae (321) | Anelloviridae (151) | Anelloviridae (82) |
| 2E | E | Healthy | 2 | N/A | N/A | Circoviridae (16) |
| Pool E | E | Diarrhoeic | 1.1 | Anelloviridae (12) | Anelloviridae (10) | Anelloviridae (3) |
| Circoviridae (1) | Circoviridae (1) | Circoviridae (4) | ||||
| 1F | F | Healthy | 3 | Picornaviridae (6) | Picornaviridae (1) | Picornaviridae (9) |
| Circoviridae (51) | Circoviridae (36) | Circoviridae (64) | ||||
| N/A | N/A | Caliciviridae (5) | ||||
| 2F | F | Healthy | 2 | Picornaviridae (1) | N/A | Picornaviridae (6) |
| N/A | N/A | Circoviridae (21) | ||||
| Pool F | F | Diarrhoeic | 2.1 | Picornaviridae (674) | Picornaviridae (411) | Picornaviridae (365) |
| N/A | N/A | Caliciviridae (108) | ||||
| N/A | Picobirnaviridae (4) | N/A | ||||
| 1G | G | Healthy | 2 | Parvoviridae (222) | Parvoviridae (186) | Parvoviridae (10) |
| Picornaviridae (1755) | Picornaviridae (955) | Picornaviridae (936) | ||||
| N/A | N/A | Caliciviridae (97) | ||||
| Circoviridae (52) | N/A | Circoviridae (39) | ||||
| 2G | G | Healthy | 2 | Picornaviridae (183389) | Picornaviridae (85080) | Picornaviridae (92805) |
| Circoviridae (9) | Circoviridae (24) | Circoviridae (121) | ||||
| N/A | N/A | Caliciviridae (16108) | ||||
| Pool G | Diarrhoeic | 2.6 | Picornaviridae (2) | Picornaviridae (2) | Picornaviridae (2) | |
| 1H | H | Healthy | 2 | N/A | Circoviridae (1) | Circoviridae (11) |
| 2H | H | Healthy | 3 | Picornaviridae (20) | Picornaviridae (15) | Picornaviridae (20) |
| N/A | N/A | Circoviridae (323) | ||||
| Pool H | H | Diarrhoeic | 2.6 | N/A | N/A | Reoviridae (5) |
| 1I | I | Healthy | 3 | Adenoviridae (1) | Adenoviridae (1) | Adenoviridae (29) |
| Circoviridae (6) | Circoviridae (12) | Circoviridae (57) | ||||
| Pool I | I | Diarrhoeic | 1.9 | Picornaviridae (133) | Picornaviridae (69) | Picornaviridae (64) |
| N/A | N/A | Caliciviridae (2) | ||||
| N/A | Circoviridae (1) | N/A | ||||
| 1J | J | Healthy | 1 | N/A | Circoviridae (6) | Circoviridae (25) |
| 2J | J | Healthy | 1 | N/A | Circoviridae (25) | Circoviridae (24) |
| N/A | N/A | Parvoviridae (3) | ||||
| Adenoviridae (1) | N/A | Adenoviridae (2) | ||||
| Pool J | Diarrhoeic | 0.8 | N/A | N/A | Circoviridae (4) |
a Age in days for individual piglets. For pooled samples, the average age is given.
b Reads classified as homologous to viral nucleotide sequences by Kraken reported on family level.
c Reads classified as homologous to viral proteins using Diamonds BLASTx settings reported on family level.
d Reads classified as homologous to viral protein families in the vFam database reported on viral family level.