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

Niczyporuk, Jowita Samanta; Kozdruń, Wojciech; Tomczyk, Grzegorz; Piekarska, Karolina; Barabasz, Marcin; Michalski, Marcin

doi:10.2478/jvetres-2024-0028

Figures & Tables

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
Nucleotide sequence	Parameters	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
Nucleotide sequence	Parameters	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
Flock from farm	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	P_s	ϕ	π	D
14	487	0.974000	0.306276	0.431275	1.846440

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

Figures & Tables

Fig 1.

Pair-wise distance with overall mean distance

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

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

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

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

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

Tajima’s neutrality test results

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