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

Monika Olech
Monika Olech
, 
Jacek Kuźmak
Jacek Kuźmak
, 
Anna Kycko
Anna Kycko
 and 
Andrzej Junkuszew
Andrzej Junkuszew
   | Nov 15, 2022
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Published Online: Nov 15, 2022
Page range: 497 - 510
Received: Jun 07, 2022
Accepted: Nov 03, 2022
DOI: https://doi.org/10.2478/jvetres-2022-0064
Keywords
© 2022 M. Olech et al. published by Sciendo
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

Fig. 1

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
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

Fig. 2

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
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

Fig. 3

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
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

Fig. 4

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
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

Fig. 5

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
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

Fig. 6

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
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
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