Phylogenetic analysis of small ruminant lentiviruses originating from naturally infected sheep and goats from Poland based on the long terminal repeat sequences

Olech, Monika; Kuźmak, Jacek; Kycko, Anna; Junkuszew, Andrzej

doi:10.2478/jvetres-2022-0064

Figures & Tables

Neighbour-joining phylogenetic tree based on the alignment of the long terminal repeat fragment. Sequences from this study are labelled by coloured circles (red – subtype A17; green – subtype A5; orange – subtype A23; pink – subtypes A18 and A13; brown – subtypes A16 and A1; yellow – subtype A27; blue – subtype A24; light blue – A12; black – unassigned) and their names are preceded by the flock origin and the animal species (s – sheep; g – goat). Reference small ruminant lentivirus strains are shown by name followed by GenBank accession number and subtype. Numbers at the branches indicate the percentage of bootstrap values obtained from 1,000 replicates

Maximum-likelihood phylogenetic tree based on the alignment of the long terminal repeat fragment. Sequences from this study are labelled by coloured circles (red – subtype A17; green – subtype A5; orange – subtypes A23 and A1; pink – subtypes A18 and A13; brown – subtype A16; yellow – subtype A27; blue – subtype A24; light blue – A12; black – unassigned) and their names are preceded by the flock origin and the animal species (s – sheep; g – goat). Reference small ruminant lentivirus strains are shown by name followed by GenBank accession number and subtype. Numbers at the branches indicate the percentage of bootstrap values obtained from 1,000 replicates

Unweighted pair group with arithmetic means phylogenetic tree based on the alignment of the long terminal repeat fragment. Sequences from this study are labelled by coloured circles (red – subtype A17; green – subtype A5; orange – subtype A23; pink – subtypes A18 and A13; brown – subtypes A16 and A1; yellow – subtype A27; blue – subtype A24; light blue – A12; black – unassigned) and their names are preceded by the flock origin and the animal species (s – sheep; g – goat). Reference small ruminant lentivirus strains are shown by name followed by GenBank accession number and subtype. Numbers at the branches indicate the percentage of bootstrap values obtained from 1,000 replicates

WebLogo for alignment of long terminal repeat sequences of small ruminant lentivirus strains belonging to groups A, B, C and D. The heights of the letters are a measure of how well conserved the residues are. The boundaries between U3, R and U5 are indicated by arrows. Transcription factor AML (vis), AP-1, AP-4 TATA box and polyadenylation signal (poly A) binding sites are shown in boxes

Alignment of U3-R sequences of the long terminal repeat region from Polish small ruminant lentivirus (SRLV) strains. Sequences are aligned against the prototype K1514 and Cork strains representative of SRLV groups A and B, respectively. Dots indicate identity with Cork, and dashes represent gaps. Boundaries between U3, R and U5 are indicated by straight arrows. AP-1, AP-4 and AML (vis) motifs, the TATA box and polyadenylation signal (poly A) are marked by boxes

The BootScan analysis of recombination in the alignments. The analysis was performed with the pairwise distance model with a window size of 200, step size of 20 and 1,000 bootstrap replicates by the RPD4 program. a – recombination even in almost all subtype A12 strains; b – recombination event in all subtype A5 strains

Information on the samples characterised in the present study

Sample	Flock	Type of flock	Voivodeship	Host	Strain	Subtype gag	Subtype env	Proposed subtype LTR	GenBank accession number
1	1	Single-	Małopolskie	sheep	0016	A13	A13	unassigned	ON637582
		species
		Single-
2	2	species	Małopolskie	sheep	209	A1	A1	N/A	N/A
3		Single-		goat	90472	A1	A1	A1	ON637581
4	3		Podkarpackie	goat	90960	A1	A1	N/A	N/A
5		species		goat	90281	A1	A1	N/A	N/A
6				sheep	11	B2	B2	N/A	N/A
7		Single-		sheep	2437	B2	B2	N/A	N/A
8	4	species	Lubelskie	sheep	4106	B2	B2	N/A	N/A
9				sheep	4084	B2	B2	N/A	N/A
10				sheep	Tryk2	A12	A12	A12	ON637584
11				sheep	5	A12	N/A	N/A	N/A
12		Mixed-		sheep	Tryk6	A12	A12	A12	ON637583
13	5	species	Lubelskie	sheep	10	A12	N/A	N/A	N/A
14				sheep	13	B2	A12/B2	N/A	N/A
15				sheep	15	A12	A12	N/A	N/A
16				goat	2461	B1	B1	N/A	N/A
17	6	Single-	Małopolskie	goat	2462	B1	B1	N/A	N/A
18		species		goat	2466	B1	B1	N/A	N/A
19		Single-		goat	2991	B1/A1	B1	N/A	N/A
20	7	species	Podkarpackie	goat	2993	A16	A16	A16	ON637585
21	8	Single-	Podlaskie	goat	1202	A12/A	B2/A12	A16	ON637586
22		species		goat	1203	A	B1/A1/A12	N/A	N/A
23				goat	3085	A17	A17	A17	ON637551
24				goat	1561	A17	A17	A17	ON637545
25				goat	8370	A17	A17	A17	ON637608
26				goat	5616	A17	A17	A17	ON637546
27				goat	0042	A17	A17	A17	ON637541
28				goat	8344	A17	A17	A17	ON637553
29		Single-		goat	5675	A17	A17	A17	ON637554
30	9	species	Mazowieckie	goat	1485	A17	A17	A17	ON637547
31				goat	1580	A17	A17	A17	ON637548
32				goat	5686	A17	A17	A17	ON637544
33				goat	8172	A17	A17	A17	ON637549
34				goat	5621	A17	A17	A17	ON637543
35				goat	6909	A17	A17	A17	ON637542
36				goat	9431	A17	A17	A17	ON637540
37				goat	5654	A17	A17	A17	ON637550
38				sheep	6922	A13	N/A	A13	ON637573
39		Mixed-		sheep	8063	A13	N/A	A13	ON637576
40	10	species	Małopolskie	sheep	9179	A13	N/A	A13	ON637575
41				sheep	7041	A18	N/A	A18	ON637589
42				sheep	0090	A18	N/A	A18	ON637588
43	11	Mixed-	Małopolskie	sheep	7010	A18	N/A	N/A	N/A
44		species		sheep	7020	A18	N/A	A18	ON637587
45				sheep	6981	A13	N/A	A13	ON637580
46				sheep	9155	A13	N/A	A13	ON637578
47		Mixed-		sheep	1406	A13	N/A	A13	ON637579
48	12	species	Małopolskie	sheep	4742	A18	N/A	N/A	N/A
49				sheep	1304	A13	N/A	A13	ON637574
50				sheep	1911	A13	N/A	A13	ON637577
51				goat	5826	A5	A5	A5	ON637566
52				goat	5819	A5	A5	A5	ON637568
53				goat	4742	A5	A5	A5	ON637569
54				goat	7592	A5	A5	A5	ON637567
55	13	Single-species	Podkarpackie	goat	5962	A5	A5	A5	ON637565
56				goat	5994	A5	A5	A5	ON637570
57				goat	6038	A5	A5	A5	ON637572
58				goat	3038	A5	A5	A5	ON637571
59				goat	5870	A5	A5	A5	ON637564
60				goat	7134	A12	A12	A12	ON637562
61				goat	7102	A12	A12	A12	ON637561
62		Mixed-		goat	6808	A12	A12	A12	ON637560
63	14		Wielkopolskie	goat	7096	A12	A12	A12	ON637559
64		species		goat	8891	A12	A12	A12	ON637557
65				goat	7219	A12	A12	A12	ON637558
66				sheep	0334	B2	N/A	A5	ON637563
67				goat	3540	B2	B2	A5	ON637599
68				goat	0580	B2	B2	A12	ON637552
69				goat	0788	B2	N/A	A5	ON637605
70				goat	9509	A12	A12	A12	ON637606
71				goat	9510	A12/B2	A12	A12	ON637602
72				goat	3533	A12	A12	A12	ON637609
73				goat	3535	A12/B2	A12	A5	ON637607
74				goat	0599	B2	A	A5/A12	ON637603/ON637604
75				goat	8699	A12	A12	A12	ON637601
76				sheep	1	A12	A12	A24	ON637590
77		Mixed-		sheep	3	A12	A12	unassigned	ON637594
78	15	species	Lubelskie	sheep	14	A12/B2	B2	A24	ON637600
79				sheep	20	B2	B2	A5	ON637598
80				sheep	21	B2	B2	N/A	N/A
81				sheep	29	B2	N/A	N/A	N/A
82				sheep	4	A12	N/A	A24	ON637591
83				sheep	6	A12	N/A	A24	ON637597
84				sheep	13	A12	A12	unassigned	ON637595
85				sheep	16	A12	A12	unassigned	ON637596
86				sheep	33	A12	A12	unassigned	ON637593
87				sheep	12	A12	A12	N/A	N/A
88				sheep	40	A12	A12	unassigned	ON637592
89				sheep	3225	A24	N/A	A24	ON637623
90		Mixed-		sheep	3188	A24	A24	A24	ON637622
91	16	species	Podkarpackie	sheep	3249	A24	A24	A24	ON637621
92				sheep	3201	A24	A24	N/A	N/A
93				sheep	3275	B2	A23	A23	ON637610
94				sheep	3691	B2	B	unassigned	ON637612
95				sheep	4018	A23	B	unassigned	ON637613
96				sheep	2590	A23/B2	A23	A23	ON637614
97				sheep	4315	A23/B2	A23	A23	ON637615
98	17	Mixed-	Podkarpackie	sheep	1622	A23	A23	A23	ON637616
99		species		goat	8046	A5	N/A	A5	ON637617
100				goat	8039	A5	N/A	A5	ON637618
101				goat	8008	A5	A5	A5	ON637619
102				goat	9692	A5	A5	A5	ON637620
103				goat	1318	A5	N/A	A5	ON637611
104				sheep	9855	B2	B	A18	ON637539
105	18	Mixed-	Podkarpackie	goat	4464	A	N/A	A18	ON637556
106		species		sheep	5023	A24	A	A5	ON637555
107				goat	goat2	A27	N/A	A27	OM517095
108				goat	goat3	A27	N/A	A27	OM517100
109		Single-	Warmińsko-	goat	goat4	A27	N/A	A27	OM517105
110	19	species	Mazurskie	goat	goat5	A27	N/A	A27	OM517114
111				goat	goat6	A27	N/A	A27	OM517117
112				goat	goat7	A27	N/A	A27	OM517122

Phylogenetic analysis of small ruminant lentiviruses originating from naturally infected sheep and goats from Poland based on the long terminal repeat sequences

Figures & Tables

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Information on the samples characterised in the present study

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