Phylogenetic Analysis of Belgian Small Ruminant Lentiviruses Supports Cross Species Virus Transmission and Identifies New Subtype B5 Strains
Abstract
:1. Introduction
2. Results
2.1. Analysis of the Current SRLV Phylogeny
2.2. Phylogeny of Belgian SRLV Strains in the Gag-Pol Region
2.3. Phylogeny of Belgian SRLV Strains in the Pol Region
3. Discussion
4. Materials and Methods
4.1. Sample Selection
4.2. DNA Extraction, PCR Amplification, and Sequencing
4.3. Multiple Alignments and Phylogenetic Analysis
4.4. Recombination Analysis
5. Conclusions
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Subtypes | Genomic Regions Used for the Classification | Year | Species in Which the Subtype Was Detected | Country of Origin | References |
---|---|---|---|---|---|
A1 | gag-pol (1.8 kb) pol (1.2 kb) RT (279 bp) | 2004 | Sheep | Iceland | [7] |
A2 | 2004 | Sheep | North America | [7] | |
A3 | 2004 | Sheep and goats | Switzerland | [7] | |
A4 | 2004 | Sheep and goats | Switzerland | [7] | |
A5 | 2004 | Goats | Switzerland | [7] | |
A6 | RT (279 bp) | 2004 | Sheep and goats | Southern France | [7] |
A7 | pol (1.2 kb) | 2004 | Goats | Switzerland | [7] |
A8 | gag (684 bp) | 2007 | Goats | Italy | [15] |
A9 | gag (684 bp) | 2007 | Sheep and goats | Italy | [15] |
A10 | pol (353 bp) | 2010 | Goats | Italy | [16] |
A11 | gag-pol (640 bp) | 2011 | Sheep and goats | Italy | [17] |
A12 | CA (467 bp) MA(327 bp) SU (394 bp) | 2012 | Sheep and goats | Poland | [12] |
A13 | Sheep and goats | Poland | [12] | ||
A14 | gag-pol (1471 bp) pol (1025 bp) | 2013 | Goats | Slovenia | [18] |
A15 | 2013 | Sheep | Slovenia | [18] | |
A16 | CA (467 bp) env (344 bp) | 2018 | Goats | Poland | [11] |
A17 | 2018 | Goats | Poland | [11] | |
A18 * | gag (576 bp) | 2019 | Sheep | Poland | [19] |
A18 * | Full genome partial gag gene | 2019 | Goat | Italy | [20] |
A19 | 2019 | Sheep | Italy | [20] | |
B1 | gag-pol (1.8 kb) pol (1.2 kb) RT (279 bp) | 2004 | Sheep and goats | U.S | [7] |
B2 | 2004 | Sheep | Switzerland | [7] | |
B3 | gag-pol (1320 bp) pol (3201 bp) env (2814 bp) | 2011 | Sheep and goats | Italy | [21] |
B4 | gag (1187 bp) | 2013 | goats | Canada | [22] |
C | gag-pol (1.8 kb) pol (1.2 kb) RT (279 bp) | 2004 | Sheep and goats | Norway | [7] |
D | pol (1.2 kb) | 2004 | Sheep and goats | Switzerland | [7] |
E1 | gag (525 bp) | 2010 | Goats | Italy | [23] |
E2 | gag (525 bp) | 2010 | Goats | Italy | [23] |
Animal Identification | Species | Type of Farm Activity | Mixed Herds with Sheep and Goats | Farms Size (Number of Animals) | Province (Belgium) | Ct Values Obtained in qPCR | Gag-Pol Subtype | Genetic Distances to the Closest Reference Strains (MVV1514/CAEV Cork) for the Gag-Pol Fragment * | Pol Subtype | Genetic Distances to the Closest Reference Strains (MVV1514/CAEV Cork) for the Pol Fragment * |
---|---|---|---|---|---|---|---|---|---|---|
A.3.4 | Sheep | Hobby | Yes | 7 | Antwerp | Neg | A1 (MN784764) | 17.02% | A1 (MN784784) | 17.63% |
H.4.2 | Sheep | Hobby | No | 17 | Hainaut | Neg | B1 (MN784761) | 10.47% | N.O | |
LB.1.6 | Sheep | Professional | No | 65 | Limburg | 32.91 | A1 (MN784760) | 16.10% | A1 (MN784782) | 16.75% |
LK.3.3 | Sheep | Hobby | No | 7 | Liege | 33.25 | A1 (MN784758) | 15.95% | A1 (MN784779) | 17.83% |
LK.5.4 | Sheep | Hobby | No | 23 | Liege | 32.29 | A1 (MN784757) | 15.74% | A1 (MN784778) | 18.12% |
LK.6.3 | Sheep | Professional | No | 150 | Liege | 34.14 | A1 (MN784756) | 14.81% | A1 (MN784777) | 17.43% |
LX.2.1 | Sheep | Professional | No | 226 | Luxembourg | 29.1 | A1 (MN784755) | 15.17% | A1 (MN784776) | 18.41% |
OV.1.7 | Sheep | Hobby | No | 15 | East Flanders | 35.13 | A1 (MN784754) | 15.10% | A1 (MN784775) | 17.43% |
OV.13.1 | Sheep | Hobby | No | 10 | East Flanders | 33.08 | A1 (MN784752) | 14.60% | A1 (MN784774) | 18.51% |
OV.20.1 | Sheep | Hobby | No | 15 | East Flanders | 34.1 | A1 (MN784751) | 15.67% | A1 (MN784773) | 16.85% |
VB.1.2 | Sheep | Hobby | No | 12 | Flemish Brabant | 36.82 | A1 (MN784750) | 15.53% | A1 (MN784771) | 18.41% |
VB.3.1 | Sheep | Hobby | Yes | 7 | Flemish Brabant | Neg | N.O a | N.O | ||
VB.7.7 | Sheep | Hobby | No info | 7 | Flemish Brabant | 32.35 | A1 (MN784748) | 16.24% | A1 (MN784772) | 17.43% |
WV.4.3 | Sheep | Hobby | No | 10 | West Flanders | 35.28 | A1 (MN784746) | 16.38% | A1 (MN784767) | 16.94% |
WV.14.5 | Sheep | Professional | No info | 200 | West Flanders | 35.06 | A1 (MN784744) | 14.46% | A1 (MN784769) | 17.43% |
H.1.6 | Goat | Hobby | Yes | 10 | Hainaut | 40 | B1 (MN784763) | 11.25% | N.O | |
H.2.6 | Goat | Professional | No | 100 | Hainaut | 36.78 | B1 (MN784762) | 12.39% | B1 (MN784783) | 13.22% |
LB.2.3 | Goat | Hobby | No | 3 | Limburg | 32.55 | B1 (MN784759) | 12.25% | B5 (MN784781) | 13.12% |
LK.3.1 | Goat | Hobby | No | 4 | Liege | 40 | N.O | A1 (MN784780) | 18.90% | |
OV.4.5 | Goat | Hobby | Yes | 15 | East Flanders | 38.97 | N.O | N.O | ||
OV.7.7 | Goat | Professional | No | 70 | East Flanders | 37.42 | B1 (MN784753) | 12.11% | N.O | |
VB.5.6 | Goat | Professional | Yes | 100 | Flemish Brabant | 36.65 | B1 (MN784749) | 12.89% | B5 (MN784770) | 13.22% |
WV.3.2 | Goat | Hobby | No | 3 | West Flanders | 36.7 | B1 (MN784747) | 12.54% | B1 (MN784768) | 13.12% |
WV.7.1 | Goat | Professional | Yes | 347 | West Flanders | 40 | N.O | A1 (MN784766) | 18.22% | |
WV.12.3 | Goat | Hobby | No | 10 | West Flanders | 34.12 | B1 (MN784745) | 11.32% | B1 (MN784765) | 12.63% |
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Michiels, R.; Adjadj, N.R.; De Regge, N. Phylogenetic Analysis of Belgian Small Ruminant Lentiviruses Supports Cross Species Virus Transmission and Identifies New Subtype B5 Strains. Pathogens 2020, 9, 183. https://doi.org/10.3390/pathogens9030183
Michiels R, Adjadj NR, De Regge N. Phylogenetic Analysis of Belgian Small Ruminant Lentiviruses Supports Cross Species Virus Transmission and Identifies New Subtype B5 Strains. Pathogens. 2020; 9(3):183. https://doi.org/10.3390/pathogens9030183
Chicago/Turabian StyleMichiels, Rodolphe, Nadjah Radia Adjadj, and Nick De Regge. 2020. "Phylogenetic Analysis of Belgian Small Ruminant Lentiviruses Supports Cross Species Virus Transmission and Identifies New Subtype B5 Strains" Pathogens 9, no. 3: 183. https://doi.org/10.3390/pathogens9030183