Table 1.
Characteristics of viRNAs expressed in RVFV-infected mosquito cells; evolution during acute and persistent infection in Aag2 cells
| Small-RNA library | RVFV RNA segment | Time p.i. (h) | Reads aligning to RVFV genome |
||||||
|---|---|---|---|---|---|---|---|---|---|
| Total reads |
Reads with mismatches (%) |
||||||||
| No. total (unique) | Avg length (nt) | Avg quality scorea | No. (%): |
0 | ≥1 | ||||
| Genomic sense | Antigenomic sense | ||||||||
| Aag-2 | L segment | Mock infection | 21,888 (16,682) | 10.63 | 35.44 | 7,274 (33.2) | 15,624 (71.3) | 528 (2.41) | 21,360 (97.6) |
| 24 | 54,195 (53,682) | 19.11 | 36.23 | 23,308 (43) | 31,092 (57.3) | 41,911 (77.3) | 12,284 (22.6) | ||
| 48 | 124,516 (119,998) | 18.66 | 36.53 | 61,825 (49.6) | 63,929 (51.3) | 92,358 (74.2) | 32,158 (25.8) | ||
| 72 | 312,657 (306,790) | 23.68 | 36.67 | 112,001 (35.8) | 201,910 (64.6) | 282,132 (90.2) | 30,525 (9.8) | ||
| Passage 3 | 609,884 (593,874) | 23.01 | 36.69 | 336,885 (55.2) | 281,208 (46.1) | 553,914 (90.8) | 55,970 (9.2) | ||
| M segment | Mock infection | 10,352 (9,450) | 11.33 | 34.75 | 6,625 (64) | 4,228 (40.8) | 527 (5.1) | 9,825 (94.9) | |
| 24 | 355,721 (355,353) | 22.77 | 36.37 | 190,798 (53.6) | 165,063 (46.4) | 341,638 (96) | 14,083 (4) | ||
| 48 | 678,728 (675,733) | 21.51 | 36.6 | 349,433 (51.5) | 330,379 (48.7) | 639,250 (94.2) | 39,478 (5.8) | ||
| 72 | 2,265,853 (2,249,092) | 24.34 | 36.63 | 1,045,619 (46.1) | 1,222,596 (53.9) | 2,185,093 (96.4) | 80,760 (3.6) | ||
| Passage 3 | 1,469,089 (1,458,095) | 24.05 | 36.58 | 936,518 (63.7) | 535,245 (36.4) | 1,408,329 (95.9) | 60,760 (4.1) | ||
| S segment | Mock infection | 4,338 (4,139) | 11.78 | 35.08 | 1,435 (33.1) | 2,975 (68.6) | 446 (10.3) | 3,892 (89.7) | |
| 24 | 472,666 (464,823) | 19.61 | 35.92 | 56,205 (11,9) | 416,499 (88.1) | 454,575 (96.2) | 18,091 (3.8) | ||
| 48 | 1,147,187 (1,136,372) | 18.83 | 36.07 | 81,385 (7.1) | 1,065,959 (92.9) | 1,102,611 (96.1) | 44,576 (3.9) | ||
| 72 | 2,412,216 (2,407,348) | 23.12 | 36.37 | 164,089 (6.8) | 2,248,302 (93.2) | 2,340,636 (97) | 71,580 (3) | ||
| Passage 3 | 2,828,925 (2,824,469) | 22.93 | 36.5 | 187,089 (6.6) | 2,641,998 (93.4) | 2,742,861 (97) | 86,064 (3) | ||
| U4.4 | L segment | Mock infection | 23,802 (16,542) | 10.7 | 35.22 | 19,110 (80.3) | 7,281 (30.6) | 627 (2.6) | 23,175 (97.3) |
| 48 | 153,413 (151,045) | 23.2 | 36.14 | 73,141 (47.7) | 81,092 (52.8) | 138,236 (90.1) | 15,177 (9.9) | ||
| M segment | Mock infection | 17,856 (14,417) | 10.54 | 34.71 | 8,646 (48.4) | 9,616 (53.8) | 579 (3.2) | 17,277 (96.8) | |
| 48 | 1,967,446 (1,966,524) | 24.95 | 36.28 | 1,300,017 (66) | 667,784 (33.9) | 1,855,337 (94.3) | 112,109 (5.7) | ||
| S segment | Mock infection | 6,386 (6,120) | 11.48 | 34.72 | 1,485 (23.2) | 4,955 (77.6) | 890 (13.9) | 5,496 (86.1) | |
| 48 | 2,114,814 (2,113,941) | 25.06 | 36.1 | 257,160 (12.1) | 1,857,749 (87.8) | 2,020,445 (95.5) | 94,369 (4.5) | ||
| C6/36 | L segment | Mock infection | 17,784 (11,576) | 10.6 | 35.4 | 13,011 (73.1) | 7,515 (42.3) | 787 (4.4) | 16,997 (95.6) |
| 48 | 47,428 (44,986) | 15.86 | 32.9 | 24,092 (50.8) | 24,541 (51.7) | 30,441 (64.2) | 16,987 (35.8) | ||
| M segment | Mock infection | 13,259 (12,627) | 10.96 | 35.1 | 5,117 (38.6) | 8,531 (64.3) | 601 (4.5) | 12,658 (95.5) | |
| 48 | 198,265 (196,710) | 17.28 | 33.45 | 133,373 (67.2) | 66,138 (33.3) | 176,283 (88.9) | 21,982 (11.1) | ||
| S segment | Mock infection | 9,343 (9,148) | 11.66 | 35.72 | 3,064 (32.8) | 6,318 (67.6) | 882 (9.4) | 8,461 (90.6) | |
| 48 | 134,035 (133,678) | 17.27 | 32.99 | 25,488 (19) | 108,613 (81) | 118,869 (88.7) | 15,166 (11.4) | ||
a
Quality score represents an average of the confidence in each sequenced nucleotide in each viRNA.