Background
Results and discussion
Biological characterization of isolates
Isolate number | District of origin | MDT (hrs) | ICPI | F0 cleavage site motif (Pos: 111–118) | Accession # for full HN gene | Accession # for full F gene | Pathotype |
---|---|---|---|---|---|---|---|
NDV/chicken/Uganda/MU001/2011 | MASAKA | 46.2 | 1.75 | GRRQKR’FV | HG937535 | HG937567 | V |
NDV/chicken/Uganda/MU004/2011 | MASAKA | 46.4 | 1.76 | GRRQKR’FV |
1
|
2
| V |
NDV/chicken/Uganda/MU005/2011 | MASAKA | 47.8 | 1.77 | GRRQKR’FV |
1
|
2
| V |
NDV/chicken/Uganda/MU007/2011 | MASAKA | 46 | 1.76 | GRRQKR’FV | HG937536 | HG937568 | V |
NDV/chicken/Uganda/MU009/2011 | MASAKA | 48 | 1.78 | GRRQKR’FV | HG937537 | HG937569 | V |
NDV/chicken/Uganda/MU010/2011 | MASAKA | 46.8 | 1.79 | GRRQKR’FV | HG937538 | HG937570 | V |
NDV/chicken/Uganda/MU013/2011+ | MUKONO | 80.1 | 0.35 | GRRQKR’FV | HG937539 | HG937571 | M |
NDV/chicken/Uganda/MU014/2011* | MUKONO | 54.2 | 1.77 | GRRQKR’FV | HG937540 | V | |
NDV/chicken/Uganda/MU019/2011 | WAKISO | 68.8 | 1.68 | GRRQKR’FV | HG937541 | HG937572 | M |
NDV/chicken/Uganda/MU022/2011* | ABIM | 44.8 | 1.77 | GRRQKR’FV | HG937542 | V | |
NDV/chicken/Uganda/MU024/2011 | ABIM | ND | ND | GRRQKR’FV | HG937573 | ||
NDV/chicken/Uganda/MU026/2011 | BUGIRI | 74.5 | 1.61 | GRRQKR’FV | HG937543 | HG937574 | M |
NDV/chicken/Uganda/MU028/2011 | BUGIRI | 40.2 | 1.79 | GRRQKR’FV |
3
|
4
| V |
NDV/chicken/Uganda/MU029/2011* | BUGIRI | 40.1 | 1.78 | GRRQKR’FV | HG937544 | V | |
NDV/chicken/Uganda/MU030/2011* | IGANGA | 36.8 | 1.78 | GRRQKR’FV | HG937545 | V | |
NDV/chicken/Uganda/MU031/2011* | IGANGA | 46.9 | 1.78 | GRRQKR’FV | HG937546 | V | |
NDV/chicken/Uganda/MU032/2011 | IGANGA | 36.8 | 1.77 | GRRQKR’FV | HG937575 | V | |
NDV/chicken/Uganda/MU033/2011 | IGANGA | 40.2 | 1.78 | GRRQKR’FV | HG937576 | V | |
NDV/chicken/Uganda/MU035/2011 | IGANGA | 44.2 | 1.75 | GRRQKR’FV | HG937547 | HG937577 | V |
NDV/chicken/Uganda/MU037/2011 | KOTIDO | 68.2 | 1.7 | GRRQKR’FV | HG937578 | M | |
NDV/chicken/Uganda/MU038/2011* | KOTIDO | 71.2 | 1.69 | GRRQKR’FV | M | ||
NDV/chicken/Uganda/MU039/2011 | KUMI | 48.6 | 1.7 | GRRQKR’FV | HG937548 | HG937579 | V |
NDV/chicken/Uganda/MU040/2011 | KUMI | 58.9 | ND | GRRQKR’FV | HG937580 | V | |
NDV/chicken/Uganda/MU044/2011 | NAMUTUMBA | 56.8 | 1.66 | GRRQKR’FV | HG937581 | V | |
NDV/chicken/Uganda/MU050/2011 | ARUA | 50.6 | 1.75 | GRRQKR’FV | HG937582 | V | |
NDV/chicken/Uganda/MU052/2011* | ARUA | 38.4 | 1.8 | GRRQKR’FV | HG937550 | V | |
NDV/chicken/Uganda/MU054/2011* | ARUA | 38.4 | 1.82 | GRRQKR’FV | HG937551 | V | |
NDV/chicken/Uganda/MU056/2011 | ARUA | 54.4 | 1.67 | GRRQKR’FV | HG937552 | HG937583 | V |
NDV/chicken/Uganda/MU058/2011* | ARUA | 34.6 | 1.78 | GRRQKR’FV | HG937535 | V | |
NDV/chicken/Uganda/MU059/2011* | ARUA | 48.2 | 1.76 | GRRQKR’FV | HG937553 | V | |
NDV/duck/Uganda/MU062/2011 | ARUA | 58 | 1.74 | GRRQKR’FV | HG937584 | V | |
NDV/chicken/Uganda/MU063/2011 | ARUA | 48.6 | 1.76 | GRRQKR’FV |
5
| V | |
NDV/chicken/Uganda/MU069/2011 | KIRYANDONGO | 42.3 | 1.79 | GRRQKR’FV | HG937554 | HG937585 | V |
NDV/chicken/Uganda/MU071/2011 | KIRYANDONGO | 48.8 | 1.75 | GRRQKR’FV | HG937555 | HG937586 | V |
NDV/chicken/Uganda/MU072/2011* | KIRYANDONGO | 38.2 | 1.79 | GRRQKR’FV | HG937556 | V | |
NDV/chicken/Uganda/MU074/2011 | KOBOKO | 48.2 | 1.77 | GRRQKR’FV | HG937557 | HG937587 | V |
NDV/chicken/Uganda/MU077/2011* | KOBOKO | 51.1 | 1.75 | GRRQKR’FV | HG937558 | V | |
NDV/chicken/Uganda/MU083/2011* | NEBBI | 48.2 | 1.76 | GRRQKR’FV | HG937559 | V | |
NDV/chicken/Uganda/MU084/2011 | NEBBI | 64.2 | 1.62 | GRRQKR’FV | HG937560 | HG937588 | M |
NDV/chicken/Uganda/MU090/2011 | GULU | 46.2 | 1.77 | GRRQKR’FV | HG937561 | HG9375689 | V |
NDV/chicken/Uganda/MU091/2011* | GULU | 44.3 | 1.83 | GRRQKR’FV | HG937562 | V | |
NDV/chicken/Uganda/MU096/2011* | GULU | 56.5 | ND | GRRQKR’FV | HG937563 | V | |
NDV/chicken/Uganda/MU098/2011* | GULU | 44.2 | 1.77 | GRRQKR’FV | HG937564 | V | |
NDV/chicken/Uganda/MU099/2011* | GULU | 50.2 | 1.75 | GRRQKR’FV |
6
| V | |
NDV/chicken/Uganda/MU102/2011* | GULU | 37.6 | 1.79 | GRRQKR’FV |
7
| V | |
NDV/chicken/Uganda/MU105/2011* | GULU | 55.7 | 1.74 | GRRQKR’FV |
7
| V | |
NDV/chicken/Uganda/MU108/2011* | KABALE | 49.8 | 1.72 | GRRQKR’FV | HG937565 | V | |
NDV/chicken/Uganda/MU111/2011 | KASESE | 52.1 | 1.86 | GRRQKR’FV | HG937566 | HG937590 | V |
NDV/chicken/Uganda/MU113/2011 | KASESE | 56.4 | ND | GRRQKR’FV | HG937591 | V |
Phylogenetics analysis of Ugandan NDV isolates
Genotype (number of sequences analyzed) | I | II | III | IV | IX | V | VI | VII | XII | VIII | X | XI | XIII | XIV | XVI | XVII | XVIII |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
I (n = 113) |
0.009
|
0.009
|
0.008
|
0.008
|
0.011
|
0.010
|
0.012
|
0.010
|
0.008
|
0.013
|
0.011
|
0.011
|
0.013
|
0.011
|
0.012
|
0.012
| |
II (n = 128) | 0.118 |
0.010
|
0.010
|
0.010
|
0.013
|
0.012
|
0.014
|
0.011
|
0.009
|
0.015
|
0.014
|
0.013
|
0.017
|
0.013
|
0.014
|
0.013
| |
III (n = 9) | 0.103 | 0.118 |
0.008
|
0.009
|
0.011
|
0.010
|
0.012
|
0.010
|
0.010
|
0.013
|
0.012
|
0.011
|
0.014
|
0.011
|
0.013
|
0.011
| |
IV (n = 6) | 0.101 | 0.115 | 0.074 |
0.008
|
0.010
|
0.009
|
0.011
|
0.008
|
0.010
|
0.010
|
0.011
|
0.010
|
0.012
|
0.009
|
0.011
|
0.011
| |
IX (n = 25) | 0.104 | 0.120 | 0.081 | 0.073 |
0.011
|
0.010
|
0.012
|
0.010
|
0.010
|
0.012
|
0.012
|
0.011
|
0.014
|
0.011
|
0.012
|
0.011
| |
V (n = 124)
|
0.179
|
0.193
|
0.163
|
0.140
|
0.161
|
0.009
|
0.010
|
0.009
|
0.013
|
0.014
|
0.011
|
0.010
|
0.012
|
0.010
|
0.011
|
0.010
| |
VI (n = 139) | 0.161 | 0.179 | 0.149 | 0.120 | 0.148 |
0.144
|
0.009
|
0.008
|
0.011
|
0.013
|
0.008
|
0.008
|
0.011
|
0.009
|
0.010
|
0.009
| |
VII (n = 312) | 0.170 | 0.195 | 0.154 | 0.133 | 0.157 |
0.158
| 0.124 |
0.010
|
0.013
|
0.015
|
0.009
|
0.009
|
0.011
|
0.011
|
0.010
|
0.009
| |
XII (n = 8) | 0.139 | 0.154 | 0.125 | 0.097 | 0.121 |
0.131
| 0.106 | 0.119 |
0.011
|
0.013
|
0.009
|
0.008
|
0.011
|
0.009
|
0.010
|
0.010
| |
VIII (n = 4) | 0.104 | 0.109 | 0.118 | 0.114 | 0.114 |
0.185
| 0.166 | 0.175 | 0.151 |
0.014
|
0.013
|
0.012
|
0.015
|
0.012
|
0.013
|
0.013
| |
X (n = 19) | 0.177 | 0.188 | 0.161 | 0.115 | 0.151 |
0.206
| 0.197 | 0.212 | 0.181 | 0.185 |
0.015
|
0.014
|
0.017
|
0.013
|
0.015
|
0.015
| |
XI (n = 4) | 0.171 | 0.193 | 0.154 | 0.135 | 0.155 |
0.160
| 0.114 | 0.103 | 0.114 | 0.173 | 0.211 |
0.007
|
0.010
|
0.011
|
0.008
|
0.008
| |
XIII (n = 27) | 0.167 | 0.189 | 0.154 | 0.129 | 0.146 |
0.154
| 0.121 | 0.105 | 0.115 | 0.173 | 0.203 | 0.096 |
0.009
|
0.010
|
0.008
|
0.007
| |
XIV (n = 52) | 0.203 | 0.234 | 0.197 | 0.170 | 0.196 |
0.184
| 0.150 | 0.140 | 0.151 | 0.208 | 0.250 | 0.126 | 0.126 |
0.013
|
0.010
|
0.010
| |
XVI (n = 4) | 0.151 | 0.172 | 0.142 | 0.111 | 0.139 |
0.152
| 0.138 | 0.154 | 0.118 | 0.157 | 0.191 | 0.150 | 0.141 | 0.180 |
0.012
|
0.011
| |
XVII (n = 54) | 0.171 | 0.202 | 0.172 | 0.149 | 0.162 |
0.161
| 0.136 | 0.127 | 0.134 | 0.182 | 0.216 | 0.114 | 0.112 | 0.127 | 0.164 |
0.008
| |
XVIII (n = 15) | 0.176 | 0.189 | 0.163 | 0.145 | 0.155 |
0.159
| 0.122 | 0.119 | 0.127 | 0.178 | 0.208 | 0.104 | 0.101 | 0.125 | 0.159 | 0.104 |
Genotype (number of sequences analyzed) | Vd | Va | Vb | Vc |
---|---|---|---|---|
Vd (n = 25)
|
0.011
|
0.008
|
0.010
| |
Va (n = 45) |
0.128
|
0.007
|
0.006
| |
Vb (n = 33) |
0.101
| 0.101 |
0.007
| |
Vc (n = 5) |
0.118
| 0.066 | 0.093 |
Genetic diversity of NDV in Uganda
Conclusions
Methods
Sample collection
Virus isolation and identification
Newcastle disease virus confirmation by RT-PCR
Biological characterization
Sequencing of the fusion (F) and hemagglutinin-neuraminidase (HN) genes
Gene | Forward primer (5′ to 3′) | Reverse primer (5′ to 3′) | PCR product (bp) |
---|---|---|---|
F | NDVF1F1: GCAAGATGGGCYCCAAACC | NDVF1R2: CATCTTCCCAACTGCCACT | 550 |
NDVF2F2: GACCACTTTACTCACTCCTC | NDVF2R1: GTAGGTGGCACGCATATTATT | 642 | |
NDVF3F2: CGACTCACAGACTCAACTC | NDVF3R2: TATARGTAATRAGRGCRGATG | 685 | |
NDVF4F2: GCAAGATRACAACATGTAGRTG | NDVF4R2: CTTGGCTAACYGCRCGGTCCAT | 709 | |
HN | NDVHN1F2: GGCTTCMCAACATCCGTTCTAC | NDVHN1R2: GAATGYGAGTGATCTCTGCA | 652 |
NDVHN2F2: CATGAGYRCTACCCAYTACTG | NDVHN2R2: GATAGATAAGATGGCYTGCTG | 591 | |
NDVHN3F2: GGGTGGCAAAYTACCCAGGAG | NDVHN3R2: GTATTGGATATTTCRGCAATGC | 768 | |
NDVHN4F2: GCATACACGACATCGACATG | NDVHN4R2: CGGTARCCCAGTYAATTTCCA | 513 |