Table 2.
Template counts and intra-host diversity of KSHV repeats in tumors and oral swabs from sixteen individuals.
| Number of samples | Templates | TRU counts | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| PtIDa | Region | Tumor | Oral | Total | Intra-host consensus length (bp) | SNV | Longest poly-G | Tumor | Oral | Total | Intra-host consensus in DR1 | Fraction of templatesb | Intra-host consensus in DR2 | Fraction of templatesb | Pairwise identityd (per cent) |
| U003 | IR1 | 1 | 0 | 1 | 4 | 0 | 4 | 2,615 | 1 | 8 | 58 | 3/4 | 6 | 1 | 99.7 |
| U004 | IR1 | 2 | 0 | 2 | 34, 24 | 0 | 58 | 2,354 | 11 | 8 | 48 | 48/58 | 4c | 1 | 99.7 |
| U007 | IR1 | 1 | 1 | 2 | 8 | 2 | 10 | 2,736 | 4 | 10–11 | 62c | 8/10 | 7 | 1 | 97.2 |
| U008 | IR1 | 2 | 1 | 3 | 11, 2 | 2 | 15 | 2,364 | 2 | 10 | 47 | 1 | 5 | 1 | 100.0 |
| U020 | IR1 | 2 | 1 | 3 | 3, 13 | 1 | 17 | 2,113 | 3 | 15–20 | 34 | 14/20 | 6 | 17/20 | 98.7 |
| U021 | IR1 | 2 | 0 | 2 | 52, 67 101 | 0 | 119 | 1,876 | 10 | 11–14 | 20 | 68/119 | 6 | 1 | 98.9 |
| U030 | IR1 | 1 | 0 | 1 | 21 | 0 | 21 | 2,043 | 4 | 8 | 21 | 21/21 | 9 | 1 | 100.0 |
| U032 | IR1 | 1 | 0 | 1 | 3 | 0 | 3 | 2,279 | 1 | 8 | 45 | 1 | 4 | 1 | 100.0 |
| U034 | IR1 | 2 | 0 | 2 | 7, 9 | 0 | 16 | 2,184 | 0 | 11–13 | 38 | 15/16 | 5 | 1 | 99.9 |
| U048 | IR1 | 2 | 0 | 2 | 28, 62 | 0 | 90 | 1,897 | 4 | 16–19 | 17 | 1 | 9 | 1 | 99.9 |
| U156 | IR1 | 2 | 0 | 2 | 31, 92 | 0 | 123 | 2,215 | 11 | 8 | 38 | 95/110 | 6 | 109/110 | 97.7 |
| U191 | IR1 | 1 | 0 | 1 | 15 | 0 | 15 | 2,383 | 6 | 13–25 | 46 | 1 | 7 | 1 | 99.8 |
| U210 | IR1 | 1 | 0 | 1 | 31 | 0 | 31 | 2,521 | 3 | 8–9 | 39 | 20/32 | 16c | 26/32 | 91.1 |
| U215 | IR1 | 1 | 0 | 1 | 46 | 0 | 46 | 1,898 | 6 | 11–14 | 25 | 1 | 5 | 44/47 | 99.7 |
| U216 | IR1 | 1 | 0 | 1 | 132 | 0 | 126 | 1,754 | 4 | 9–12 | 15 | 126/127 | 7 | 126/127 | 99.9 |
| U217 | IR1 | 1 | 1 | 2 | 20 | 2 | 22 | 1,603 | 2 | 9 | 11c | 12/23 | 5 | 19/23 | 90.7 |
| (Sum), median | (23) | (4) | (27) | 21.5 | 2,200 | 98.3 | 98.3 | ||||||||
| DR5 | DR6 | ||||||||||||||
| U003 | IR2 | 1 | 1 | 2 | 1 | 1 | 2 | 2,372 | 0 | 11 | 19 | 1 | 10 | 1 | 100.0 |
| U004 | IR2 | 2 | 1 | 3 | 34, 1 | 3 | 38 | 2,355 | 7 | 10–11 | 21 | 37/40 | 13 | 30/40 | 98.4 |
| U007 | IR2 | 1 | 1 | 2 | 17 | 3 | 20 | 1,992 | 1 | 7 | 15 | 1 | 6 | 1 | 100.0 |
| U008 | IR2 | 1 | 1 | 2 | 2 | 3 | 5 | 2,224 | 0 | 8 | 18 | 1 | 8 | 1 | 100.0 |
| U020 | IR2 | 1 | 0 | 1 | 3 | 0 | 3 | 2,415 | 1 | 7 | 28 | 2/3 | 11 | 1 | 99.5 |
| U021 | IR2 | 2 | 0 | 2 | 12, 25 | 0 | 37 | 2,227 | 5 | 7 | 23 | 26/39 | 8 | 26/39 | 96.7 |
| U030 | IR2 | 1 | 0 | 1 | 74 | 0 | 74 | 1,946 | 10 | 8 | 17 | 1 | 3c | 1 | 100.0 |
| U032 | IR2 | 1 | 0 | 1 | 4 | 0 | 4 | 2,100 | 1 | 9 | 18 | 1 | 8 | 1 | 100.0 |
| U034 | IR2 | 1 | 0 | 1 | 7 | 0 | 7 | 2,252 | 0 | 9–10 | 23 | 1 | 9 | 1 | 100.0 |
| U048 | IR2 | 2 | 0 | 2 | 31, 108 | 0 | 139 | 2,224 | 10 | 8–10 | 17 | 132/139 | 13c | 1 | 99.9 |
| U156 | IR2 | 2 | 0 | 2 | 29, 9 | 0 | 38 | 2,385 | 3 | 10–12 | 33c | 33/34 | 5 | 1 | 99.8 |
| U191 | IR2 | 1 | 0 | 1 | 6 | 0 | 6 | 2,206 | 1 | 7 | 19 | 5/6 | 12 | 1 | 99.7 |
| U210 | IR2 | 1 | 0 | 1 | 56 | 0 | 56 | 1,849 | 1 | 11–13 | 3c | 1 | 12 | 59/61 | 99.9 |
| U215 | IR2 | 1 | 0 | 1 | 19 | 0 | 19 | 1,896 | 2 | 6–8 | 8 | 1 | 9 | 1 | 99.3 |
| U216 | IR2 | 1 | 0 | 1 | 88 | 0 | 88 | 2,252 | 11 | 7 | 22 | 72/84 | 10 | 1 | 99.7 |
| U217 | IR2 | 1 | 0 | 1 | 33 | 0 | 33 | 2,084 | 1 | 7 | 13 | 31/32 | 8 | 1 | 99.9 |
| (Sum), median | (20) | (4) | (24) | 27 | 2,226 | 99.6 | |||||||||
| U003 | LANAr | 1 | 0 | 1 | 1 | 0 | 1 | 1,693 | – | – | – | ||||
| U004 | LANAr | 2 | 1 | 3 | 30, 40 | 6 | 76 | 1,492 | 9 | N/A | 99.9 | ||||
| U007 | LANAr | 1 | 1 | 2 | 17 | 12 | 29 | 1,489 | 1 | N/A | 100.0 | ||||
| U008 | LANAr | 2 | 1 | 3 | 27, 6 | 13 | 46 | 1,183 | 3 | N/A | 99.8 | ||||
| U020 | LANAr | 2 | 1 | 3 | 2, 13 | 1 | 16 | 1,741 | 2 | N/A | 100.0 | ||||
| U021 | LANAr | 2 | 0 | 2 | 46, 67 | 0 | 113 | 1,522 | 6 | N/A | 100.0 | ||||
| U030 | LANAr | 1 | 0 | 1 | 91 | 0 | 91 | 1,567 | 6 | N/A | 99.9 | ||||
| U032 | LANAr | 1 | 0 | 1 | 8 | 0 | 8 | 1,807 | 1 | N/A | 99.9 | ||||
| U034 | LANAr | 2 | 0 | 2 | 5, 12 | 0 | 17 | 1,456 | 1 | N/A | 100.0 | ||||
| U048 | LANAr | 2 | 0 | 2 | 37, 131 | 0 | 168 | 1,909 | 24 | N/A | 99.8 | ||||
| U156 | LANAr | 2 | 0 | 2 | 86, 36 | 0 | 122 | 1,624 | 9 | N/A | 100.0 | ||||
| U191 | LANAr | 2 | 0 | 2 | 5, 1 | 0 | 6 | 1,735 | 1 | N/A | 100.0 | ||||
| U210 | LANAr | 1 | 0 | 1 | 59 | 0 | 59 | 1,636 | 4 | N/A | 100.0 | ||||
| U215 | LANAr | 1 | 0 | 1 | 21 | 0 | 21 | 1,741 | 2 | N/A | 94.1 | ||||
| U216 | LANAr | 1 | 0 | 1 | 76 | 0 | 76 | 1,909 | 6 | N/A | 94.3 | ||||
| U217 | LANAr | 0 | 0 | 0 | 0 | 0 | 0 | – | – | – | – | ||||
| (Sum), median | (23) | (4) | (27) | 38.5 | 1,636 | 99.1 | |||||||||
| Total (medians) | 21.5 | 2.5 | 26.5 | ||||||||||||
a
PtID—participant identifier.
b
The fraction of templates with the intra-host consensus TRU count divided by the total number of sequenced templates obtained.
c
Includes mismatches and gap versus non-gap sites but excluding gap versus gap sites; the bolded values indicate ≥99.9 per cent pairwise identity.
d
The most or least number of TRU counts.