Table 4.
SARS-CoV-2 competition in deer co-infected with lineage A and B.1.1.7 strains determined by next generation sequencing
| 4 DPC | 18 DPC | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| #108 | #905 | #106 | #919 | #49 | #50 | |||||||
| Sample | %WA1 | %B.1.1.7 | %WA1 | %B.1.1.7 | %WA1 | %B.1.1.7 | %WA1 | %B.1.1.7 | %WA1 | %B.1.1.7 | %WA1 | %B.1.1.7 |
| Nasal Swab 0 DPC | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND |
| Nasal Swab 1 DPC | 1.7% | 98.3% | 40.0% | 60.0% | 0.7% | 99.3% | 15.8% | 84.2% | ND | ND | ND | ND |
| Nasal Swab 3 DPC | 0.0% | 100.0% | 0.0% | 100.0% | 0.0% | 100.0% | 0.0% | 100.0% | LMR | LMR | NT | NT |
| Nasal Swab 4 DPC | 0.0% | 100.0% | 0.0% | 100.0% | NT | NT | NT | NT | NT | NT | NT | NT |
| Nasal Swab 5 DPC | NT | NT | NT | NT | 0.0% | 100.0% | LMR | LMR | LMR | LMR | LMR | LMR |
| Nasal Swab 7 DPC | NT | NT | NT | NT | LMR | LMR | LMR | LMR | 0.0% | 100.0% | LMR | LMR |
| Nasal Swab 10 DPC | NT | NT | NT | NT | ND | ND | NT | NT | LMR | LMR | ND | ND |
| Oral Swab 0 DPC | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND |
| Oral Swab 1 DPC | 5.4% | 94.6% | 51.0% | 49.0% | LMR | LMR | ND | ND | ND | ND | ND | ND |
| Oral Swab 3 DPC | 0.0% | 100.0% | ND | ND | 0.0% | 100.0% | ND | ND | LMR | LMR | ND | ND |
| Oral Swab 4 DPC | 0.0% | 100.0% | 2.9% | 97.1% | NT | NT | NT | NT | NT | NT | NT | NT |
| Oral Swab 5 DPC | NT | NT | NT | NT | 0.0% | 100.0% | ND | ND | ND | ND | 0.0% | 100.0% |
| Oral Swab 7 DPC | NT | NT | NT | NT | ND | ND | NT | NT | 0.0% | 100.0% | NT | NT |
| Oral Swab 10 DPC | NT | NT | NT | NT | ND | ND | ND | ND | ND | ND | ND | ND |
| Rectal Swab 0 DPC | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND |
| Rectal Swab 1 DPC | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND | LMR | LMR |
| Rectal Swab 3 DPC | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND |
| Rectal Swab 4 DPC | ND | ND | ND | ND | NT | NT | NT | NT | NT | NT | NT | NT |
| Rectal Swab 5 DPC | NT | NT | NT | NT | NT | NT | NT | NT | NT | NT | ND | ND |
| Rectal Swab 7 DPC | NT | NT | NT | NT | ND | ND | NT | NT | ND | ND | ND | ND |
| Rectal Swab 10 DPC | NT | NT | NT | NT | ND | ND | ND | ND | ND | ND | ND | ND |
| Nasal Wash | 0.0% | 100.0% | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND |
| BALF | 0.0% | 100.0% | 1.3% | 98.7% | ND | ND | ND | ND | ND | ND | ND | ND |
| Conche | 0.0% | 100.0% | LMR | LMR | NT | NT | NT | NT | NT | NT | NT | NT |
| Ethnoturbinates | 0.0% | 100.0% | 0.0% | 100.0% | NT | NT | NT | NT | ND | ND | NT | NT |
| Nasopharynx | 3.9% | 96.1% | 20.9% | 79.1% | 4.1% | 95.9% | 13.8% | 86.2% | NT | NT | LMR | LMR |
| Trachea, rostal | 0.0% | 100.0% | 0.0% | 100.0% | NT | NT | ND | ND | NT | NT | ND | ND |
| Trachea, middle | 0.0% | 100.0% | NT | NT | NT | NT | NT | NT | NT | NT | ND | ND |
| Trachea, distal | 0.0% | 100.0% | 0.0% | 100.0% | NT | NT | ND | ND | NT | NT | ND | ND |
| Bronchi | 0.0% | 100.0% | 0.0% | 100.0% | NT | NT | ND | ND | ND | ND | ND | ND |
| Lung, left cranial A | 0.0% | 100.0% | 0.0% | 100.0% | ND | ND | ND | ND | ND | ND | ND | ND |
| Lung, left cranial B | NT | NT | NT | NT | ND | ND | ND | ND | ND | ND | ND | ND |
| Lung, left caudal | NT | NT | NT | NT | ND | ND | ND | ND | ND | ND | ND | ND |
| Lung, right cranial | 0.0% | 100.0% | 0.0% | 100.0% | ND | ND | NT | NT | ND | ND | ND | ND |
| Lung, right caudal | 0.0% | 100.0% | 0.0% | 100.0% | ND | ND | ND | ND | ND | ND | ND | ND |
| Lung, right middle | NT | NT | NT | NT | ND | ND | ND | ND | ND | ND | ND | ND |
| Accessory | 0.0% | 100.0% | 0.0% | 100.0% | ND | ND | ND | ND | ND | ND | ND | ND |
| Tonsil | 0.0% | 100.0% | LMR | LMR | 1.2% | 98.8% | NT | NT | ND | ND | LMR | LMR |
| Prescapular LN | NT | NT | ND | ND | ND | ND | ND | ND | ND | ND | NT | NT |
| Tracheobronchial LN | 0.0% | 100.0% | LMR | LMR | ND | ND | ND | ND | ND | ND | NT | NT |
| Cranial mediastinal LN | NT | NT | NT | NT | ND | ND | ND | ND | ND | ND | ND | ND |
| Mesenteric LN | 1.0% | 99.0% | NT | NT | NT | NT | NT | NT | NT | NT | ND | ND |
| Ileocecal LN | NT | NT | NT | NT | NT | NT | ND | ND | ND | ND | ND | ND |
| Retropertioneal LN | NT | NT | 0.9% | 99.1% | ND | ND | ND | ND | ND | ND | ND | ND |
| Gastrohepatic LN | NT | NT | NT | NT | ND | ND | ND | ND | ND | ND | ND | ND |
| Submandibular LN | NT | NT | LMR | LMR | ND | ND | ND | ND | ND | ND | ND | ND |
| Retropharyengeal LN | 0.2% | 99.8% | NT | NT | NT | NT | ND | ND | 0.3% | 99.7% | LMR | LMR |
| Spleen | 0.0% | 100.0% | LMR | LMR | ND | ND | NT | NT | ND | ND | ND | ND |
| Liver | NT | NT | NT | NT | ND | ND | ND | ND | ND | ND | ND | ND |
| Heart | 0.0% | 100.0% | 0.0% | 100.0% | ND | ND | ND | ND | ND | ND | ND | ND |
| Kidney | 3.5% | 96.5% | 0.0% | 100.0% | ND | ND | NT | NT | ND | ND | ND | ND |
| Bone Marrow | NT | NT | ND | ND | ND | ND | ND | ND | ND | ND | NT | NT |
| Stomach | ND | ND | NT | NT | ND | ND | ND | ND | ND | ND | ND | ND |
| Small Intestine | NT | NT | LMR | LMR | ND | ND | ND | ND | NT | NT | ND | ND |
| Large Intestine | 0.0% | 100.0% | NT | NT | NT | NT | ND | ND | ND | ND | ND | ND |
| Ileocecal Junction | NT | NT | NT | NT | ND | ND | ND | ND | ND | ND | ND | ND |
| Brain | 2.9% | 97.1% | LMR | LMR | ND | ND | ND | ND | ND | ND | ND | ND |
| Olfactory Bulb | NT | NT | NT | NT | ND | ND | ND | ND | ND | ND | ND | ND |
WA1=USA-WA1/2020 strain; B.1.1.7=USA/CA-5574/2020 strain; LN=lymph node; NT=not tested; ND=not detected; LMR=low mapped reads