Molecular Characterization of African Swine Fever Virus Isolates in Estonia in 2014–2019
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sampling
2.2. Selection of Isolates for Molecular Characterization
2.3. Detection of the Genome of ASFV
2.4. B602L Gene Amplification and Sequencing
2.5. Phylogenetic Analysis
2.6. Mapping Software and Spatial Autocorrelation
3. Results
3.1. B602L Gene Amplification and Sequencing
3.2. Phylogenetic Analysis
3.3. Geographic Distribution of CVR Variants
4. Discussion
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Year | 2014 | 2015 | 2016 | 2017 | 2018 | 2019 | CVR% * | ||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
County | PCR | CVR | PCR | CVR | PCR | CVR | PCR | CVR | PCR | CVR | PCR | CVR | |
Harju | 0 | 0 | 0 | 0 | 35 | 6 | 66 | 12 | 17 | 2 | 0 | 0 | 16.9 |
Ida-Viru | 4 | 3 | 10 | 2 | 22 | 3 | 3 | 1 | 4 | 4 | 4 | 2 | 31.9 |
Jõgeva | 0 | 0 | 55 | 6 | 146 | 14 | 0 | 0 | 1 | 0 | 0 | 0 | 9.9 |
Järva | 0 | 0 | 98 | 9 | 95 | 5 | 0 | 0 | 0 | 0 | 0 | 0 | 7.3 |
Lääne | 0 | 0 | 0 | 0 | 57 | 13 | 97 | 16 | 10 | 2 | 1 | 0 | 18.8 |
L-Viru | 0 | 0 | 82 | 6 | 171 | 9 | 42 | 4 | 0 | 0 | 0 | 0 | 6.4 |
Põlva | 0 | 0 | 227 | 6 | 166 | 2 | 9 | 4 | 3 | 1 | 0 | 0 | 3.2 |
Pärnu | 0 | 0 | 23 | 3 | 76 | 6 | 68 | 13 | 5 | 0 | 0 | 0 | 12.8 |
Rapla | 0 | 0 | 6 | 2 | 181 | 6 | 51 | 7 | 1 | 0 | 0 | 0 | 6.3 |
Saare | 0 | 0 | 0 | 0 | 90 | 8 | 236 | 16 | 15 | 1 | 1 | 0 | 7.3 |
Tartu | 0 | 0 | 117 | 38 | 151 | 26 | 13 | 6 | 1 | 1 | 0 | 0 | 25.2 |
Valga | 13 | 6 | 113 | 17 | 10 | 3 | 0 | 0 | 0 | 0 | 0 | 0 | 19.1 |
Viljandi | 47 | 9 | 166 | 22 | 37 | 6 | 3 | 1 | 0 | 0 | 0 | 0 | 15.0 |
Võru | 9 | 5 | 108 | 11 | 40 | 1 | 3 | 2 | 1 | 0 | 0 | 0 | 11.8 |
TOTAL | 73 | 25 | 1005 | 122 | 1277 | 108 | 591 | 82 | 58 | 11 | 6 | 2 | 11.6 |
Size of an Amplicon (bp) | No of WB 1 | No of DP 2 | No of aa * Tetrameric Repeats | Difference From Reference Strain | CVR Variant |
---|---|---|---|---|---|
400 | 300 | 42 | 10 | no | CVR1 |
400 | 18 | 6 | 10 | G instead of A resulted in aa change Y instead of C | CVR1/SNP1 |
~350 | 17 | 0 | 7 | deletion of 3 aa tetramer repeats CASMCADTNVDT | CVR2 |
Number of Findings | |||||
---|---|---|---|---|---|
Municipality | First Finding | Last Finding | 2015 | 2016 | Total |
Rannu | 17th of July 2015 | 22nd of Feb 2016 | 5 | 2 | 7 |
Konguta | 29th of July 2015 | 6th of Nov 2015 | 4 | 0 | 4 |
Tähtvere | 29th of Sept 2015 | 29th of Mar 2016 | 2 | 1 | 3 |
Nõo | 14th of Oct 2015 | 15th of Mar 2016 | 2 | 1 | 3 |
Total | 13 | 4 | 17 |
No of Findings | ||||||
---|---|---|---|---|---|---|
County | Municipality | First Finding | Last Finding | 2016 | 2017 | Total |
Lääne | Hanila | 30th of Nov 2016 | 24th of Jan 2017 | 2 | 1 | 3 |
Nõva | 10th of Aug 2017 | 10th of Aug 2017 | 0 | 1 | 1 | |
Noarootsi | 12th of Dec 2017 | 12th of Dec 2017 | 0 | 1 | 1 | |
Harju | Keila | 5th of Jan 2017 | 4th of July 2017 | 0 | 3 | 3 |
Pärnu | Varbla | 18th of Jan 2017 | 16th of June 2017 | 0 | 2 | 2 |
Tõstamaa | 20th of Feb 2017 | 12th of Dec 2017 | 0 | 6 | 6 | |
Audru | 25th of May 2017 | 16th of June 2017 | 0 | 2 | 2 | |
Total | 2 | 16 | 18 |
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Vilem, A.; Nurmoja, I.; Niine, T.; Riit, T.; Nieto, R.; Viltrop, A.; Gallardo, C. Molecular Characterization of African Swine Fever Virus Isolates in Estonia in 2014–2019. Pathogens 2020, 9, 582. https://doi.org/10.3390/pathogens9070582
Vilem A, Nurmoja I, Niine T, Riit T, Nieto R, Viltrop A, Gallardo C. Molecular Characterization of African Swine Fever Virus Isolates in Estonia in 2014–2019. Pathogens. 2020; 9(7):582. https://doi.org/10.3390/pathogens9070582
Chicago/Turabian StyleVilem, Annika, Imbi Nurmoja, Tarmo Niine, Taavi Riit, Raquel Nieto, Arvo Viltrop, and Carmina Gallardo. 2020. "Molecular Characterization of African Swine Fever Virus Isolates in Estonia in 2014–2019" Pathogens 9, no. 7: 582. https://doi.org/10.3390/pathogens9070582