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Molecular characteristics of fowl adenovirus strains detected in broiler chickens on diets without immunostimulant supplements

Jowita Samanta Niczyporuk
Jowita Samanta Niczyporuk
, 
Wojciech Kozdruń
Wojciech Kozdruń
, 
Grzegorz Tomczyk
Grzegorz Tomczyk
, 
Karolina Piekarska
Karolina Piekarska
, 
Marcin Barabasz
Marcin Barabasz
 oraz 
Marcin Michalski
Marcin Michalski
   | 20 maj 2024
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Data publikacji: 20 maj 2024
Zakres stron: -
Otrzymano: 01 lut 2024
Przyjęty: 15 maj 2024
DOI: https://doi.org/10.2478/jvetres-2024-0028
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© 2024 Jowita Samanta Niczyporuk et al., published by Sciendo
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

Fig 1.

The constructed phylogenetic tree based on nucleotide sequences of Loop L1 region HVR1-4 of the hexon gene of fowl adenoviruses isolate obtained in the present investigation and submitted to GenBank * – Polish strains of FAdVs
The constructed phylogenetic tree based on nucleotide sequences of Loop L1 region HVR1-4 of the hexon gene of fowl adenoviruses isolate obtained in the present investigation and submitted to GenBank * – Polish strains of FAdVs

Pair-wise distance with overall mean distance

MW353019-FAdV-5/B-I-Intestinum
MW353018-FAdV-1/A-L-Liver 2.556
2.898 2.933
2.264 2.499 0.585
2.769 2.716 0.495 0.411
2.814 2.554 0.565 0.616 0.610
2.762 2.753 0.568 0.401 0.413 0.654
2.760 2.810 0.611 0.343 0.427 0.655 0.413
2.892 2.870 0.515 0.380 0.384 0.623 0.158 0.414
2.880 2.591 0.597 0.325 0.428 0.627 0.406 0.049 0.409
2.710 2.520 0.558 0.615 0.605 0.047 0.652 0.652 0.621 0.627
2.751 2.748 0.568 0.395 0.414 0.676 0.030 0.412 0.152 0.413 0.673
2.844 2.837 0.509 0.374 0.367 0.638 0.149 0.408 0.028 0.395 0.632 0.142
3.198 2.707 3.204 3.127 3.702 4.099 3.087 3.813 2.972 3.705 4.068 2.893 2.854

Maximum composite likelihood estimate of the pattern of nucleotide substitution indicating differences in the nucleotide sequences of the examined strains

A T/U C G
A - 6.58 6.92 15.17
T/U 5.55 - 10.50 7.53
C 5.55 9.98 - 7.53
G 11.18 6.58 6.92 -

Nucleotide codon composition of the 2 examined sequences and 12 sequences of adenovirus strains derived from the GenBank database

T(U) C A G Total T-1 C-1 A-1 G-1 Pos 1 T-2 C-2 A-2 G-2 Pos 2 T-3 C-3 A-3 G-3 Pos 3
1/A 24.7 27.5 18.1 29.8 896.0 33 18.4 24.7 24.1 299.0 30 33.4 14.7 22.1 299.0 11 30.5 14.8 43.3 298.0
2/D 26.0 24.9 21.0 28.0 899.0 32 16.7 24.7 27.0 300.0 33 32.7 16.0 18.7 300.0 14 25.4 22.4 38.5 299.0
3/D 25.6 25.3 19.2 30.0 908.0 31 16.5 23.4 29.4 303.3 35 29.7 16.5 18.8 303.1 11 29.8 17.5 41.7 302.0
MW353018-FAdV-1/A-L-Liver 24.0 28.1 19.3 28.6 559.0 27 36.9 12.8 23.0 187.0 14 30.5 20.3 35.3 187.0 31 16.8 24.9 27.6 185.0
MW353019-FAdV-5/B-I-Intestinum 22.8 32.3 22.6 22.2 517.0 17 25.0 33.3 25.0 168.0 28 34.3 21.3 16.3 178.0 23 37.4 13.5 25.7 171.0
4/C 23.4 26.1 17.8 32.7 884.0 34 15.6 27.7 28.1 295.0 29 30.5 18.3 21.7 295.0 7 32.3 12.2 48.3 294.0
5/B 25.9 25.7 18.8 29.5 902.0 32 16.6 24.3 26.9 301.0 31 32.6 16.9 19.9 301.0 15 32.3 15.3 41.7 300.0
6/E 27.5 24.1 20.9 27.6 896.0 33 17.4 24.4 25.1 299.0 33 30.8 18.1 18.1 299.0 16 28.0 20.1 39.6 298.0
7/E 25.1 26.1 18.6 30.3 902.0 32 17.9 23.6 26.9 301.0 32 30.2 16.3 21.3 301.0 11 24.2 16.0 42.1 300.0
8a/E 27.0 24.6 21.7 26.7 899.0 33 17.0 24.7 25.7 300.0 32 31.3 18.3 18.3 300.0 16 30.0 22.1 36.1 299.0
9/D 23.6 26.1 17.8 32.5 884.0 34 15.6 22.7 28.1 295.0 29 31.2 18.6 21.4 295.0 9 25.4 11.9 48.0 294.0
10/C 25.9 25.7 18.7 29.6 902.0 32 17.3 23.6 27.2 301.5 31 32.2 16.6 20.3 301.0 15 31.6 16.0 41.3 300.0
11/D 25.1 25.9 17.9 31.1 898.0 31 18.0 23.7 27.0 300.0 32 30.7 16.0 21.7 300.0 12 27.7 14.1 44.6 298.0
8b/E 25.9 25.6 20.3 28.2 898.0 32 17.0 24.7 26.7 300.0 32 33.3 16.0 18.3 300.0 14 29.2 20.1 39.6 298.0
Avg. 25.3 26.0 19.4 29.3 846.0 31 18.3 23.8 26.6 292.1 31 31.6 17.2 20.6 282.8 14 28.2 17.1 40.7 281.1

Maximum likelihood indicated in 24 different nucleotide sequences of the examined strains, with their substitutions indicated

Nucleotide sequence Parameters Substitution
BIC AICc InL (+I) (+G) R f(A) f(T) f(C) f(G)
T92+G+I 29 9,817.521 9,619.014 −4,780.382 0.00 0.43 1.25 0.228 0.228 0.272 0.272
HKY+G+I 31 9,828.001 9,615.822 −4,776.768 0.00 0.41 1.29 0.209 0.247 0.260 0.283
TN93+G+I 32 9,830.888 9,611.875 −4,773.785 0.00 0.41 1.33 0.209 0.247 0.260 0.283
K2+G+I 28 9,853.291 9,661.621 −4,802.694 0.00 0.45 1.20 0.250 0.250 0.250 0.250
GTR+G+I 35 9,853.608 9,614.092 −4,771.865 0.00 0.42 1.33 0.209 0.247 0.260 0.283
T92+G 28 9,875.288 9,683.618 −4,813.693 n/a 1.33 1.01 0.228 0.228 0.272 0.272
KHY+G 30 9,887.801 9,682.458 −4,811.096 n/a 1.32 1.02 0.209 0.247 0.260 0.283
T93+G 31 9,893.237 9,681.058 −4,809.387 n/a 1.33 1.02 0.209 0.247 0.260 0.283
JC+G+I 27 9,902.143 9,717.311 −4,831.547 0.00 0.50 0.50 0.250 0.250 0.250 0.250
K2+G 27 9,905.582 9,720.750 −4,833.267 n/a 1.37 0.98 0.250 0.250 0.250 0.250
CTR+G 34 9,909.610 9,676.927 −4,804.292 n/a 1.32 1.02 0.209 0.247 0.260 0.283
JC+G 26 9,945.931 9,767.937 −4,857.868 n/a 1.41 0.50 0.250 0.250 0.250 0.250
T92 27 10,086.086 9,901.254 −4,923.519 n/a n/a 0.98 0.228 0.228 0.272 0.272
T92+I 28 10,090.277 9,898.607 −4,921.187 0.01 n/a 1.02 0.228 0.228 0.272 0.272
HKY 29 10,103.858 9,904.644 −4,923.197 n/a n/a 0.50 0.209 0.247 0.260 0.283
K2 26 10,104.355 9,925.864 −4,936.831 n/a n/a 0.85 0.250 0.250 0.250 0.250
HKI+I 30 10,107.250 9,899.012 −4,919.373 0.02 n/a 0.87 0.209 0.247 0.260 0.283
TN93 30 10,108.001 9,901.711 −4,920.722 n/a n/a 0.86 0.209 0.247 0.260 0.283
K2+I 27 10,111.923 9,922.418 −4,934.100 0.01 n/a 0.86 0.250 0.250 0.250 0.250
TN93+I 31 10,113.216 9,895.822 −4,916.768 0.02 n/a 0.87 0.209 0.247 0.260 0.283
GTR 33 10,111.923 9,886.075 −4,909.876 n/a n/a 0.87 0.290 0.247 0.260 0.283
GTR+I 34 10,113.216 9,880.533 −4,906.095 0.02 n/a 0.87 0.209 0.247 0.260 0.283
JC 25 10,130.574 9,959.419 −4,954.616 n/a n/a 0.50 0.250 0.250 0.250 0.250
JC+I 26 10,136.144 9,958.150 −4,952.975 0.01 n/a 0.50 0.250 0.250 0.250 0.250
Nucleotide sequence Parameters Substitution
r(AT) r(AC) r(AG) r(TA) r(TC) r(TG) r(CA) r(CT) r(CG) r(GA) r(GT) r(GC)
T92+G+I 29 0.050 0.060 0.152 0.050 0.152 0.060 0.050 0.127 0.060 0.127 0.050 0.060
HKY+G+I 31 0.054 0.056 0.160 0.045 0.147 0.061 0.045 0.140 0.061 0.118 0.054 0.056
TN93+G+I 32 0.053 0.055 0.202 0.044 0.115 0.600 0.044 0.110 0.060 0.149 0.053 0.055
K2+G+I 28 0.057 0.057 0.136 0.057 0.136 0.057 0.057 0.136 0.057 0.136 0.057 0.057
GTR+G+I 35 0.055 0.043 0.201 0.047 0.116 0.049 0.034 0.111 0.080 0.148 0.043 0.073
T92+G 28 0.057 0.068 0.137 0.057 0.137 0.068 0.057 0.115 0.068 0.115 0.057 0.068
KHY+G 30 0.061 0.064 0.144 0.051 0.132 0.070 0.051 0.126 0.070 0.106 0.061 0.064
T93+G 31 0.061 0.064 0.168 0.051 0.112 0.070 0.051 0.106 0.070 0.124 0.061 0.064
JC+G+I 27 0.083 0.083 0.083 0.083 0.083 0.083 0.083 0.083 0.083 0.083 0.083 0.083
K2+G 27 0.063 0.063 0.124 0.063 0.124 0.063 0.063 0.124 0.063 0.124 0.063 0.063
CTR+G 34 0.052 0.050 0.168 0.044 0.112 0.061 0.040 0.107 0.098 0.124 0.053 0.090
JC+G 26 0.083 0.083 0.083 0.083 0.083 0.083 0.083 0.083 0.083 0.083 0.083 0.083
T92 27 0.061 0.073 0.126 0.061 0.126 0.073 0.061 0.106 0.073 0.106 0.061 0.073
T92+I 28 0.061 0.073 0.127 0.061 0.127 0.073 0.061 0.106 0.073 0.106 0.061 0.073
HKY 29 0.066 0.069 0.132 0.056 0.121 0.076 0.056 0.115 0.076 0.097 0.066 0.069
K2 26 0.067 0.067 0.115 0.067 0.115 0.067 0.057 0.115 0.067 0.115 0.067 0.067
HKI+I 30 0.066 0.069 0.133 0.056 0.122 0.075 0.056 0.116 0.075 0.098 0.066 0.069
TN93 30 0.066 0.069 0.151 0.056 0.105 0.076 0.056 0.100 0.076 0.111 0.066 0.069
K2+I 27 0.067 0.067 0.115 0.083 0.115 0.067 0.067 0.115 0.067 0.115 0.067 0.067
TN93+I 31 0.066 0.069 0.152 0.056 0.104 0.075 0.056 0.099 0.075 0.112 0.066 0.069
GTR 33 0.048 0.052 0.153 0.041 0.106 0.070 0.042 0.101 0.110 0.113 0.061 0.101
GTR+I 34 0.048 0.053 0.154 0.041 0.106 0.069 0.043 0.101 0.110 0.113 0.060 0.102
JC 25 0.083 0.083 0.083 0.083 0.083 0.083 0.083 0.083 0.083 0.083 0.083 0.083
JC+I 26 0.083 0.083 0.083 0.083 0.083 0.083 0.083 0.083 0.083 0.083 0.083 0.083

The presence of FAdV strains in the examined Ross 308 broiler chicken flocks

Flock from farm Age
1 day old 21 days old 42 days old
AO not detected not detected not detected
P not detected not detected not detected
AO&P not detected not detected not detected
C not detected FAdVs 1/A and 5/B not detected

Analysis of the number of successive codons and relative synonymous codon usage

Codon Count RSCU Codon Count RSCU Codon Count RSCU Codon Count RSCU
UUU(F) 18 0.8 UCU(S) 21.9 0.84 UAU(Y) 9.6 0.63 UGU(C) 13.7 0.72
UUC(F) 26.9 1.2 UCC(S) 35.4 1.36 UAC(Y) 20.8 1.37 UGC(C) 24.4 1.28
UUA(L) 11.4 0.64 CA(S) 17.7 0.68 UAA(*) 12.5 0.84 UGA(*) 15.4 1.03
UUG(L) 29.2 1.63 UCG(S) 42.3 1.63 UAG(*) 16.8 1.13 UGG(W) 20.2 1.00
CUU(L) 10.9 0.61 CCU(P) 17.5 0.69 CAU(H) 11.3 0.99 CGU(R) 17.4 0.79
CUC(L) 23.6 1.32 CCC(P) 28.9 1.15 CAC(H) 11.4 1.01 CGC(R) 29.4 1.33
CUA(L) 7.8 0.43 CCA(P) 17.4 0.69 CAA(Q) 11.9 0.88 CGA(R) 18.2 0.83
CUG(L) 24.6 1.38 CCG(P) 37.1 1.47 CAG(Q) 15.1 1.12 CGG(R) 27.1 1.23
AUU(I) 11.3 0.86 ACU(T) 12.2 0.57 AAU(N) 9.9 0.65 AGU(S) 14.1 0.54
AUC(I) 19.8 1.51 ACC(T) 25.9 1.2 AAC(N) 20.6 1.35 AGC(S) 24.6 0.95
AUA(I) 8.2 0.63 ACA(T) 15.3 0.71 AAA(K) 17.9 0.94 AGA(R) 16.5 0.75
AUG(M) 22.1 1 ACG(T) 32.9 1.52 AAG(K) 20.1 1.06 AGG(R) 23.4 1.06
GUU(V) 15.5 0.73 GCU(A) 21.5 0.83 GAU(D) 11.4 0.68 GGU(G) 20.0 0.81
GUC(V) 25.6 1.21 GCC(A) 31.3 1.21 GAC(D) 21.9 1.32 GGC(G) 26.9 1.09
GUA(V) 14.4 0.68 GCA(A) 16.3 0.63 GAA(E) 19.6 0.94 GGA(G) 26.5 1.07
GUG(V) 29 1.37 GCG(A) 34.6 1.34 GAG(E) 22.1 1.06 GGG(G) 15.2 1.02

Tajima’s neutrality test results

m S Ps ϕ π D
14 487 0.974000 0.306276 0.431275 1.846440
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