Table 2.
Summary of NDV genome assembly described in the current study.
| Strain | Sample collection date | Region (location) | rRT-PCR L-test (CT) | NDV-specific reads | Median cov. depth | Consensus seq. length | % Completeness; gaps (# of missing bases at 5′-end|internal|3′-end) | Sub-genotype | Pathotyping | GenBank accession number | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| ICPIb | F protein cleavage motif | ||||||||||
| 2014-E734 | 10-Oct-18 | Morogoro (Manzese) | 16.54 | 84,480 | 1,886 | 15,045 | 99.03%; (117|0|30) | VII.2 | N/A | RRRKR↓FI | OR230617 |
| 2,110-K103 | 22-Sep-18 | Dar es Salaam (Kisutu) | 16.37 | 86,610 | 837 | 15,170 | 99.86%; (22|35|0) | V.3 | N/A | RRQKR↓FV | OR230621 |
| 1,056 | 15,169 | 99.85%; (0|11|23) | VII.2 | N/A | RRRKR↓FI | OR230622 | |||||
| 2,111-K104 | 22-Sep-18 | Dar es Salaam (Kisutu) | 16.37 | 375,478 | 9,828 | 15,192 | 100% | XIII.1.1 | N/A | RRRKR↓FI | OR230623 |
| 2,115-M581 | 5-Oct-18 | Morogoro (Mawenzi) | 17.80 | 143,124 | 3,926 | 15,190 | 99.99%; (0|0|2) | VII.2 | N/A | RRRKR↓FI | OR230624 |
| 2,144-BD117 | 24-May-19 | Dar es Salaam (Buguruni) | 16.82 | 32,728 | 631 | 15,187 | 99.97%; (0|6|5) | VII.2 | N/A | RRRKR↓FI | OR230625 |
| 2,145-CA127 | 3-May-19 | Arusha (Central) | 16.79 | 177,140 | 3,947 | 15,178 | 99.91%; (13|0|1) | VII.2 | N/A | RRRKR↓FI | OR230626 |
| 2,152-IM184 | 11-Apr-19 | Iringa (Mashine tatu) | 16.45 | 107,852 | 2,205 | 15,159 | 99.78%; (4|0|29) | VII.2 | N/A | RRRKR↓FI | OR230627 |
| 2,159-ME50 | 29-May-19 | Morogoro (Manzese) | 14.25 | 63,407 | 1,206 | 15,177 | 99.90%; (10|0|5) | VII.2 | N/A | RRRKR↓FI | OR230628 |
| 1995-B01a | 21-Sep-18 | Dar es Salaam (Buguruni) | 18.55 | 73,140 | 1,389 | 15,192 | 100% | VII.2 | N/A | RRRKR↓FI | N/A |
| 230,172 | 5,778 | 15,192 | 100% | XIII.1.1 | N/A | RRRKR↓FI | N/A | ||||
| 1996-B03 | 21-Sep-18 | Dar es Salaam (Buguruni) | 15.80 | 390,295 | 8,984 | 15,192 | 100% | VII.2 | 1.70 | RRQKR↓FV | OR230611 |
| 1997-B06 | 21-Sep-18 | Dar es Salaam (Buguruni) | 20.45 | 168,371 | 3,768 | 15,192 | 100% | VII.2 | 1.71 | RRQKR↓FV | OR230612 |
| 1998-B08AF | 21-Sep-18 | Dar es Salaam (Buguruni) | 14.92 | 471,551 | 9,928 | 15,156 | 99.76%; (0|30 + 6|30) | XIII.1.1 | 1.71 | RRRKR↓FI | OR230613 |
| 2000-B18 | 21-Sep-18 | Dar es Salaam (Buguruni) | 14.89 | 392,000 | 8,910 | 15,192 | 100% | XIII.1.1 | 1.76 | RRRKR↓FI | OR230614 |
| 2001-B20 | 21-Sep-18 | Dar es Salaam (Buguruni) | 17.13 | 16,849 | 383 | 15,084 | 99.29%; (108|95|0) | XIII.1.1 | 1.76 | RRRKR↓FI | OR230615 |
| 2007-E713 | 10-Oct-18 | Morogoro (Manzese) | 13.98 | 213,901 | 5,081 | 15,192 | 100% | VII.2 | 1.66 | RRRKR↓FI | OR230616 |
| 2015-E735 | 10-Oct-18 | Morogoro (Manzese) | 15.71 | 425,238 | 10,764 | 15,192 | 100% | VII.2 | 1.75 | RRRKR↓FI | OR230618 |
| 2016-E736 | 10-Oct-18 | Morogoro (Manzese) | 16.62 | 350,402 | 7,934 | 15,192 | 100% | VII.2 | 1.88 | RRRKR↓FI | OR230619 |
| 2017-E740 | 10-Oct-18 | Morogoro (Manzese) | 14.79 | 214,867 | 4,318 | 15,192 | 100% | VII.2 | 1.77 | RRRKR↓FI | OR230620 |
Virus intracerebral pathogenicity index (ICPI) pathotyping determined using oropharyngeal (OP) swabs from nine of the 20 chickens are shown.
a
The assembled genome sequences of the sub-genotypes VII.2 and XIII.1.1 strains identified in the chicken ID 1995-B01AF were not submitted to GenBank due to heterogeneity in various genomic positions (see text for details).
b
N/A means that the ICPI was not determined for these samples.