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

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

1 AO – flock given antibiotics in drinking water; P – flock given probiotic and prebiotic additives with vitamins and microelements in drinking water; AO&P – flock given antibiotics and probiotic and prebiotic additives with vitamins and microelements in drinking water; C – flock of controls given neither antibiotics nor probiotics, prebiotics vitamins or microelements; FAdVs – fowl adenoviruses

Table 2.

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

Table 3.

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	-

1 Each entry shows the probability of substitution (r) from one base (row) to another base (column). The sum of r values is made equal to 100. Rates of different transitional substitutions are shown in bold and those of transversional substitutions are shown in italics

Table 4.

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

1 Pos 1, Pos 2, Pos 3 – number of nucleotides in the sequences tested in the first, second, and third codon positions, respectively. The total number of nucleotides of tested strain sequences and the number of them at the codon positions are indicated by underlining. Sequences obtained from the studies are indicated in bold

Table 5.

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

1 The average number of codons was 1,303. All examined frequencies are averages over all taxa and shown as percentages. RSCU – relative synonymous codon usage

Table 6.

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

Table 7.

Tajima’s neutrality test results

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

1 m – number of sequences; S – number of segregating sites; π – nucleotide diversity; D – Tajima test statistic; ps = number of segregating sites/total number of sites (n); ϕ = number of segregating sites / total number of sites/a1

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

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DOI: https://doi.org/10.2478/jvetres-2024-0028 | Journal eISSN: 2450-8608 (formerly 2300-3235)

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Language: English

Page range: 207 - 214

Submitted on: Feb 1, 2024

Accepted on: May 15, 2024

Published on: May 20, 2024

Published by: National Veterinary Research Institute in Pulawy

In partnership with: Paradigm Publishing Services

Keywords:

adenovirus infection,

Related subjects:

Microbiology and virology,

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Veterinary medicine

© 2024 Jowita Samanta Niczyporuk, Wojciech Kozdruń, Grzegorz Tomczyk, Karolina Piekarska, Marcin Barabasz, Marcin Michalski, published by National Veterinary Research Institute in Pulawy
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

Volume 68 (2024): Issue 2 (June 2024)

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

Figures & Tables

Table. 1.

Table 2.

Table 3.

Table 4.

Table 5.

Table 6.

Table 7.

Fig 1.

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