Table 1.
Mutation frequencies identified by deep sequencing of JL-CK and RIT4385 compared to Sanger sequencing of JL-CK plaques. Unpassaged virus and virus isolated from JL-CK plaques, 10 days post-infection (d.p.i.) are shown in the top section. Virus in Vero and MDCK cell lysates, 3 d.p.i. are compared in the middle section. Mutation frequencies identified by deep sequencing of neonatal rat brains 4 d.p.i. with JL-CK virus, are shown in the lower section.
| Substrate | Virus | Mutation frequency (%) |
||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Leader | K36R | E108D | V529A | L542L | Ter550Q | L557P | N56T | C244R | P93S | F295S | E569K | D311G | ||
| Unpassaged | JL-CK | 96.7 | 9.1 | 86.6 | 27 | 26.2 | 74.2 | 26.5 | 40.5 | 97.5 | 45.3 | 27.3 | 96.9 | 43.4 |
| RIT4385 | n.d. | n.d. | n.d. | 6.2 | 16.6 | n.d. | 21.3c | n.d. | n.d. | n.d. | n.d. | n.d. | n.d. | |
| Vero Plaques# |
JL-CK | 98a | 46b | 51 | 4 | 4 | 44 | 4 | 38 | 96 | 38 | 4 | 96 | 38 |
| Vero* 3 d.p.i. |
JL-CK | 94.5 | 27.0 | 70.5 | 10.4 | 9.5 | 48.0 | 9.7 | 42.2 | 95.6 | 39.9 | 11.0 | 95.8 | 35.1 |
| RIT4385 | n.d. | n.d. | n.d. | 11.6 | 21.5 | n.d. | 30.8 | n.d. | n.d. | n.d. | n.d. | n.d. | n.d. | |
| MDCK* 3 d.p.i. |
JL-CK | 84.1 | 18.8 | 68.3 | 23.3 | 23.0 | 53.1 | 23.2 | 31.7 | 89.5 | 31.0 | 26.3 | 89.7 | 29.5 |
| RIT4385 | n.d. | n.d. | n.d. | 2.9 | 31.6 | n.d. | 33.1 | n.d. | n.d. | n.d. | n.d. | n.d. | n.d. | |
| RNV1 | JL-CK | 100 | 69.6 | 33.4 | 1.3 | 1.3 | 26.6 | 1.2 | 25.7 | 99.9 | 27.2 | 1.2 | 99.9 | 26.0 |
| RNV2 | 100 | 93.9 | 5.4 | n.d. | n.d. | 18.4 | n.d. | 5.1 | 100 | 5.8 | n.d. | 100 | 5.5 | |
| RNV3 | 100 | 94.3 | 6.6 | n.d. | n.d. | 3.1 | n.d. | 3.0 | 100 | 3.8 | 0.3 | 99.9 | 3.5 | |
#
81 plaques were sequenced except a 49 plaques and b 79 plaques due to lack of material, c Mutation in non-coding region, * data for Vero and MDCK lysates are the mean frequencies detected in 2 independent deep sequencing assays, n.d. not detected, d.p.i days post infection.