Table 1.
Virus isolates and clinical samples used for the development and evaluation of the PPRV RT-LAMP assay. Samples 1–27 were collected from the field whereas samples 28–51 were collected from the animals experimentally infected with PPRV (Morocco/2008) at The Pirbright Institute (TPI). Samples 1–12 were collected from Tanzania, 13–20 from Algeria, 21–24 from Bangladesh and 25–27 from Israel. The filter paper samples (52–54) were prepared in the lab. Samples with an asterisk are of sheep origin. CT: Cycle threshold values, TP: Time to positivity, Ta: Anneal temperature. The lineages of the PPR viruses in sample numbers 55–62 are shown in parenthesis under sample details.
| Sample No. | Sample Details | RT-qPCR Mean CT | RT-LAMP Mean Tp | RT-LAMP Mean Ta |
|---|---|---|---|---|
| 1 | Occular swab-G4 | no CT | No Tp | No Ta |
| 2 | Occular swab-G10 | 22.96 | 48.32 | 84.25 |
| 3 | Occular swab-G11 | 36.96 | 53.29 | 84.06 |
| 4 | Occular swab-G16 | 26.37 | 51.204 | 84.08 |
| 5 | Occular swab-S14* | no CT | No Tp | No Ta |
| 6 | Occular swab-S19* | no CT | No Tp | No Ta |
| 7 | Occular swab-S20* | no CT | No Tp | No Ta |
| 8 | Nasal swab-goat-1 | 37 | 55.24 | 84.11 |
| 9 | Nasal swab-goat-2 | 32 | 52.03 | 84 |
| 10 | Nasal swab-sheep-1* | 34.36 | 52.82 | 84.06 |
| 11 | Nasal swab-sheep-2* | no CT | No Tp | No Ta |
| 12 | Nasal swab-sheep-5* | 31.04 | 51.93 | 84.1 |
| 13 | Farm 1-blood 1 | 25.23 | 49.35 | 84 |
| 14 | Farm 1-blood 2 | 22.05 | 47.31 | 84.13 |
| 15 | Farm 1-blood 3 | 19.36 | 45.63 | 84.1 |
| 16 | Farm 1-blood 4 | no CT | No Tp | No Ta |
| 17 | Farm 1-blood 5 | 26.34 | 49.91 | 84.17 |
| 18 | Farm 1-blood 6 | 33.27 | 56.65 | 84.05 |
| 19 | Farm 1-blood 7 | 20.95 | 44.39 | 84.11 |
| 20 | Farm 1-blood 8 | 31.27 | 52.43 | 84.09 |
| 21 | Milk-B52/Chuadanga/2015 | 24.76 | 48.69 | 84 |
| 22 | Milk-B53/Savara/2015 | 30.1 | 50.63 | 84.06 |
| 23 | Milk-B18/Nihkanchari/2015 | 24.61 | 49.03 | 84.1 |
| 24 | Milk-B19/Nihkanchari/2015 | 23.54 | 47.17 | 84 |
| 25 | Field lung tissue-1 | 20.62 | 41.73 | 84.2 |
| 26 | Field lung tissue-2 | 28.26 | 47.23 | 84.15 |
| 27 | Field lung tissue-3 | no CT | No Tp | No Ta |
| 28 | Faecal sample-1 | noCTt | No Tp | No Ta |
| 29 | Faecal sample-2 | no CT | No Tp | No Ta |
| 30 | Faecal sample-3 | no CT | No Tp | No Ta |
| 31 | Faecal sample-4 | 19.6 | 56.575 | 84.1 |
| 32 | Faecal sample-5 | 22.45 | 58.565 | 83.94 |
| 33 | Nasal swab-1 | no CT | No Tp | No Ta |
| 34 | Nasal swab-2 | 32.65 | 58:21:00 | 83.99 |
| 35 | Nasal swab-3 | 31.22 | 58:41:00 | 84.06 |
| 36 | Nasal swab-4 | 25.18 | 48.35.00 | 84 |
| 37 | Nasal swab-5 | 28.35 | 51:06:00 | 84.19 |
| 38 | Lymp node—bronchial-1 | noCT | No Tp | No Ta |
| 39 | Lymp node—bronchial-2 | no CT | No Tp | No Ta |
| 40 | Lymp node—bronchial-3 | no CT | No Tp | No Ta |
| 41 | Lymp node—bronchial-4 | 33.24 | 54.45 | 84.18 |
| 42 | Lymp node—bronchial-5 | no CT | No Tp | No Ta |
| 43 | Lymp node—bronchial-6 | no CT | No Tp | No Ta |
| 44 | Spleen | no CT | No Tp | No Ta |
| 45 | Lymp node—mandibular | 33.92 | 50.05 | 84.09 |
| 46 | Lymp node—prescapular | no CT | No Tp | No Ta |
| 47 | Tonsil—pharyngeal | 31.08 | 45.8 | 84.05 |
| 48 | Tonsil—palatine | 32.37 | 51.73 | 84.08 |
| 49 | Ileum | no CT | No Tp | No Ta |
| 50 | Colon | no CT | No Tp | No Ta |
| 51 | Rectum | no CT | No Tp | No Ta |
| 52 | Filter paper impregnated with virus-1 | 36.12 | 56.73 | 83.99 |
| 53 | Filter paper impregnated with virus-2 | 37.23 | 58.58 | 83.94 |
| 54 | Filter paper impregnated with virus-3 | 31.92 | 54.8 | 84.08 |
| 55 | PPRV/Nigeria/75/1 (L-II) | 19.24 | 35.02 | 84.07 |
| 56 | PPRV/Nigeria/76/1 (L-II) | 23.68 | 41.09 | 84.12 |
| 57 | PPRV/Sungri/96 (L-IV) | 13.45 | 37.15 | 84.15 |
| 58 | PPRV/Ivory coast (L-I) | 20.30 | 36.8 | 84.1 |
| 59 | PPRV/IBRI-Oman (L-III) | 19.84 | 40.08 | 84 |
| 60 | PPRV/Morocco/2008 (L-IV) | 16.85 | 33.28 | 84.1 |
| 61 | PPRV/Bangladesh/170/2012 (L-IV) | 25.96 | 46.39 | 84 |
| 62 | PPRV/Ghana/78 (L-II) | 21.29 | 35.86 | 84.1 |
| 63 | Nuclease-free water (negative control) | no CT | No Tp | No Ta |
| 64 | Dolphin Morbillivirus (DMV) | no CT | No Tp | No Ta |
| 65 | Measles virus (MV) | no CT | No Tp | No Ta |
| 66 | FMDV/O/PanAsia-2 | no CT | No Tp | No Ta |
| 67 | FMDV/A/A22/Iraq 24/64 | no CT | No Tp | No Ta |
| 68 | Swine Vesicular Disease virus (SVDV) | no CT | No Tp | No Ta |