Compartmentalization of Subtype A17 of Small Ruminant Lentiviruses between Blood and Colostrum in Infected Goats Is Not Exclusively Associated to the env Gene
Abstract
:1. Introduction
2. Materials and Methods
2.1. Animals, Blood, and Colostrum Samples
2.2. PCR Technique
2.3. DNA Sequencing and Sequence Analysis
2.4. Statistical Tests for Compartmentalization
3. Results
3.1. Nucleotide and Amino Acid Sequence Distance
3.2. Phylogenetic Analysis
3.3. Nucleotide Substitutions
3.4. Existence of Compartment-Specific Signature
3.5. Tests for Compartmentalization
4. Discussion
Supplementary Materials
Author Contributions
Acknowledgments
Conflicts of Interest
References
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Goat | Compartment | gag | env | LTR | |||
---|---|---|---|---|---|---|---|
Intracompartment | Intercompartment | Intracompartment | Intercompartment | Intracompartment | Intercompartment | ||
Mean % ± SE | Mean % ± SE | Mean % ± SE | Mean % ± SE | Mean % ± SE | Mean % ± SE | ||
#8370 | PBLs | 0.4 ± 0.1 | - | 0.4 ± 0.3 | |||
CSCs | 2.0 ± 0.2 | 1.3 ± 0.1 | - | - | 0.0 ± 0.0 | 0.9 ± 0.6 | |
#1561 | PBLs | 0.7± 0.1 | 1.4 ± 0.2 | 0.5 ± 0.1 | |||
CSCs | 0.8 ± 0.1 | 0.8 ± 0.1 | 1.4 ± 0.2 | 1.8 ± 0.3 | 0.5 ± 0.2 | 0.5 ± 0.1 | |
#3085 | PBLs | 0.6 ± 0.1 | 1.3 ± 0.2 | 1.2 ± 0.4 | |||
CSCs | 0.6 ± 0.1 | 0.7 ± 0.2 | 0.7 ± 0.2 | 1.0 ± 0.2 | 0.6 ± 0.3 | 1.4 ± 0.5 |
Goat | Compartment | Gag | Env | ||
---|---|---|---|---|---|
Intracompartment | Intercompartment | Intracompartment | Intercompartment | ||
Mean % ± SE | Mean % ± SE | Mean % ± SE | Mean % ± SE | ||
#8370 | PBLs | 0.6 ± 0.2 | - | ||
CSCs | 1.0 ± 0.2 | 0.8 ± 0.1 | - | - | |
#1561 | PBLs | 0.7 ± 0.2 | 2.1 ± 0.4 | ||
CSCs | 1.1 ± 0.2 | 0.9 ± 0.1 | 2.7 ± 0.6 | 3.5 ± 0.8 | |
#3085 | PBLs | 1.1 ± 0.4 | 2.5 ± 0.5 | ||
CSCs | 0.7 ± 0.3 | 1.1 ± 0.4 | 1.3 ± 0.5 | 2.1 ± 0.5 |
Goat | Compartment | gag | env | ||||||
---|---|---|---|---|---|---|---|---|---|
dS | dN | Z-Test * | dN/dS Ratio | dS | dN | Z-Test * | dN/dS Ratio | ||
#8370 | PBLs | 0.00741 | 0.00276 | <0.128 | 0.37 | - | - | - | - |
#8370 | CSCs | 0.10837 | 0.00479 | <0.000 | 0.04 | - | - | - | - |
#1561 | PBLs | 0.02313 | 0.00276 | <0.000 | 0.12 | 0.02632 | 0.00924 | <0.013 | 0.35 |
#1561 | CSCs | 0.02185 | 0.00479 | <0.001 | 0.22 | 0.01959 | 0.01248 | <0.164 | 0.64 |
#3085 | PBLs | 0.01031 | 0.00505 | <0.077 | 0.49 | 0.01675 | 0.01147 | <0.208 | 0.68 |
#3085 | CSCs | 0.01381 | 0.00349 | <0.014 | 0.25 | 0.01029 | 0.00575 | <0.215 | 0.56 |
Goat | Genetic Region | SM | Snn | FST | rb | r | AI |
---|---|---|---|---|---|---|---|
#8370 | LTR | 1 migration | 1 | 0.751 | 0.769 | 0.756 | NS |
gag | 13 migration | 0.556 | NS | NS | 0.001 | NS | |
#1561 | env | 12 migration | 0.989 | 0.259 | 0.124 | 0.066 | 0.090 |
LTR | NS | NS | NS | NS | NS | NS | |
gag | NS | 0.817 | 0.046 | 0.025 | NS | NS | |
#3085 | env | 12 migration | 0.683 | NS | NS | −0.021 | NS |
LTR | 9 migration | 0.674 | 0.318 | 0.390 | 0.342 | NS | |
gag | 10 migration | 0.778 | 0.131 | 0.145 | 0.127 | NS |
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Olech, M.; Kuźmak, J. Compartmentalization of Subtype A17 of Small Ruminant Lentiviruses between Blood and Colostrum in Infected Goats Is Not Exclusively Associated to the env Gene. Viruses 2019, 11, 270. https://doi.org/10.3390/v11030270
Olech M, Kuźmak J. Compartmentalization of Subtype A17 of Small Ruminant Lentiviruses between Blood and Colostrum in Infected Goats Is Not Exclusively Associated to the env Gene. Viruses. 2019; 11(3):270. https://doi.org/10.3390/v11030270
Chicago/Turabian StyleOlech, Monika, and Jacek Kuźmak. 2019. "Compartmentalization of Subtype A17 of Small Ruminant Lentiviruses between Blood and Colostrum in Infected Goats Is Not Exclusively Associated to the env Gene" Viruses 11, no. 3: 270. https://doi.org/10.3390/v11030270
APA StyleOlech, M., & Kuźmak, J. (2019). Compartmentalization of Subtype A17 of Small Ruminant Lentiviruses between Blood and Colostrum in Infected Goats Is Not Exclusively Associated to the env Gene. Viruses, 11(3), 270. https://doi.org/10.3390/v11030270