Genetic Assessment of African Swine Fever Isolates Involved in Outbreaks in the Democratic Republic of Congo between 2005 and 2012 Reveals Co-Circulation of p72 Genotypes I, IX and XIV, Including 19 Variants
Abstract
:1. Introduction
2. Materials and Methods
2.1. Study Area and Samples
2.2. African Swine Fever (ASFV) DNA by Polymerase Chain Reaction (PCR)
2.3. Generation of ASFV Sequence Data
2.4. Molecular Characterization of ASFV
2.5. Central Hypervariable Region (CVR) of B602L Gene
3. Results
3.1. Clinical Findings and African Swine Fever (ASF) Diagnosis
Field Identification and Description of Collecting Localities
3.2. Laboratory Diagnostics
3.3. Molecular Characterization of ASFV
3.4. CVR of B602L Gene
3.5. Democratic Republic of the Congo (DRC) ASFV Genotypes Geographical Distribution
4. Discussion
4.1. Molecular Characterization
4.2. Disease Ecology, Molecular Epidemiology and Case Investigations
Acknowledgments
Author Contributions
Conflicts of Interest
References
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Virus | Outbreak Date | Location | GPS | Ecological Profile | Tissues | Farming System | Genotype |
---|---|---|---|---|---|---|---|
drc49/05/p1a | May 2005 | Limete | 4°18 S/15°22 E | City | Spl | Commercial | I |
drc49/05p1b | May 2005 | Limete | 4°18 S/15°22 E | City | Ln | Commercial | I |
drc49/05/P2a | May 2005 | Limete | 4°18 S/15°22 E | City | Spl | Commercial | I |
drc70/05/1 | 2005 | Limete | 4°18 S/15°22 E | City | Spl | Commercial | I |
drc75/05/1 | 2005 | Maniema | 2°93 S/25°86 E | City | Spl | Commercial | I |
drc99/05/a | 2005 | Ngafula | 4°21 S/15°14 E | Peri-urban | Spl | Commercial | I |
drcKG28110805 | Nov 2008 | Ngaliema | 4°21 S/15°21 E | City | Spl | Backyard | I |
drcKG28040802 | Apr 2008 | Kasavubu | 4°20 S/15°20 E | City | Spl | Backyard | I |
drc74/09/2 | 2009 | Nsele | 4°24 S/15°30 E | Peri-urban | Kd | Commercial | I |
drc74/09/3 | 2009 | Nsele | 4°24 S/15°30 E | Peri-urban | Lg | Commercial | I |
drc74/09/4 | 2009 | Nsele | 4°24 S/15°30 E | Peri-urban | Lv | Commercial | I |
drc74/09/6 | 2009 | Nsele | 4°24 S/15°30 E | Peri-urban | Hrt | Commercial | I |
drc94/09/2 | 2009 | Kintambo | 4°20 S/15°18 E | City | Ln | Commercial | I |
drc35/10/1 | 2010 | Ngaliema | 4°21 S/15°05 E | City | Spl | Backyard | I |
drc35/10/5 | 2010 | Ngaliema | 4°21 S/15°05 E | City | Ln | Backyard | I |
drc35/10/4 | 2010 | Ngaliema | 4°21 S/15°05 E | City | Ln | Backyard | I |
drc51/10/23 | 2010 | Ndjili | 4°24 S/15°21 E | City | Spl | Commercial | I |
drc73/10/2 | 2010 | Ngaliema | 4°21 S/15°05 E | City | Kn | Backyard | I |
drc73/10/3 | 2010 | Ngaliema | 4°21 S/15°05 E | City | Lv | Backyard | I |
drc73/10/4 | 2010 | Ngaliema | 4°21 S/15°05 E | City | Ln | Backyard | I |
drc85/10/13 | 2010 | Ngafula | 4°21 S/15°14 E | Peri-urban | Spl | Commercial | I |
drc85/10/12 | 2010 | Ngafula | 4°21 S/15°14 E | Peri-urban | Hrt | Commercial | I |
drc85/10/11 | 2010 | Ngafula | 4°21 S/15°14 E | Peri-urban | Lg | Commercial | I |
drc85/10/27 | 2010 | Ngafula | 4°21 S/15°14 E | Peri-urban | Hrt | Commercial | I |
drc85/10/25 | 2010 | Ngafula | 4°21 S/15°14 E | Peri-urban | Lv | Commercial | I |
drc86/10/1 | 2010 | Ngafula | 4°21 S/15°14 E | Peri-urban | Kd | Commercial | I |
drc86/10/3 | 2010 | Ngafula | 4°21 S/15°14 E | Peri-urban | Lv | Commercial | I |
drc108/10/3 | 2010 | Ngafula | 4°21 S/15°14 E | Peri-urban | Lv | Commercial | I |
drc108/10/5 | 2010 | Ngafula | 4°21 S/15°14 E | Peri-urban | Spl | Commercial | I |
drc27/11/1 | 2011 | Ngafula | 4°21 S/15°14 E | Peri-urban | Spl | Commercial | I |
drc27/11/2 | 2011 | Ngafula | 4°21 S/15°14 E | Peri-urban | Ln | Commercial | I |
drc27/11/3 | 2011 | Ngafula | 4°21 S/15°14 E | Peri-urban | Stm | Commercial | I |
drc27/11/5 | 2011 | Ngafula | 4°21 S/15°14 E | Peri-urban | Lv | Commercial | I |
drc65/11/2 | 2011 | Nsele | 4°24 S/15°30 E | Peri-urban | Kd | Commercial | I |
drc65/11/3 | 2011 | Nsele | 4°24 S/15°30 E | Peri-urban | Spl | Commercial | I |
drc65/11/4 | 2011 | Nsele | 4°24 S/15°30 E | Peri-urban | Lg | Commercial | I |
drc96/12/1 | 2012 | Mayanda | 5°12 S/15°14 E | Rural | Lg | Village | I |
drc96/12/2 | 2012 | Mayanda | 5°12 S/15°14 E | Rural | Spl | Village | I |
drc96/12/3 | 2012 | Mayanda | 5°12 S/15°14 E | Rural | Hrt | Village | I |
drc108/10/1 | Dec 2010 | Ngafula | 4°21 S/15°14 E | Peri-urban | Lg | Commercial | I |
drc46/11/2 | Jun 2011 | Kinshasa | 4°20 S/15°18 E | City | Hrt | Backyard | I |
drc20/07/19 | Apr 2007 | Mahagi * | 2° S/31° E | Rift Valley | Kd | Backyard | IX |
drc20/07/20 | Apr 2007 | Mahagi * | 2° S/31° E | Rift Valley | Ln | Backyard | IX |
drc25/08/3a | Mar 2008 | Boende | 0°15 S/21°01 E | Forest | Kd | Free range | IX |
drc25/08/3 | Mar 2008 | Boende | 0°15 S/21°01 E | Forest | Spl | Free range | IX |
drc25/08/42 | Mar 2008 | Boende | 0°15 S/21°01 E | Forest | Kd | Free range | IX |
drc25/08/9 | Mar 2008 | Boende | 0°15 S/21°01 E | Forest | Spl | Free range | IX |
drc35/08/1 | Apr 2008 | Boende | 0°15 S/21°01 E | Forest | Spl | Free range | IX |
drc35/08/13 | Apr 2008 | Boende | 0°15 S/21°01 E | Forest | Spl | Free range | IX |
drc35/08/P42 | Apr 2008 | Boende | 0°15 S/21°01 E | Forest | Spl | Free range | IX |
drc35/08/15 | Apr 2008 | Boende | 0°15 S/21°01 E | Forest | Spl | Free range | IX |
drc35/08/18 | Apr 2008 | Boende | 0°15 S/21°01 E | Forest | Kd | Free range | IX |
drc35/08/20 | Apr 2008 | Boende | 0°15 S/21°01 E | Forest | Spl | Free range | IX |
drc35/08/3 | Apr 2008 | Boende | 0°15 S/21°01 E | Forest | Spl | Free range | IX |
drc66/07/43 | Nov 2007 | Yakoma | 4° S/22° E | Forest | Lg | Free range | IX |
drc66/07/48 | Nov 2007 | Yakoma | 4° S/22° E | Forest | Spl | Free range | IX |
drc66/07/491 | Nov 2007 | Yakoma | 4° S/22° E | Forest | Spl | Free range | IX |
drc66/07/492 | Nov 2007 | Yakoma | 4° S/22° E | Forest | Ln | Free range | IX |
drc66/07/50 | Nov 2007 | Yakoma | 4° S/22° E | Forest | Spl | Free range | IX |
drcKG31208/3 | Dec 2008 | Lingwala | 4°20 S/15°19 E | City | Spl | Backyard | IX |
drc35/10/3 | Apr 2010 | Ngaliema | 4°21 S/15°05 E | City | Kd | Backyard | XIV |
drc21/07/22 | 2007 | Kipushi † | 12° S/28° E | City | Spl | Backyard | XIV |
Strain | Location | Year | Genotype | Tetrameric Repeats | TRS |
---|---|---|---|---|---|
drc35/10/1 | Ngaliema * | 2010 | I | AAAAAAAAAAAAAAAAAAAAAAAAAAAAABNAB NBTDBNAAAAAAAAAAAF | 51 |
drcKG28110805 | Ngaliema * | 2010 | I | AAAAAAAAABNABNBTABNAAAAAAAAAAAAAAAAA AAAAAAAAF | 45 |
drc65/11/4 | Nsele * | 2011 | I | AAAAAABNABNBTDBNAAAAAAAAF | 25 |
drc74/09/2 | Nsele * | 2009 | I | AAAAAAAAAAAAAAAAAAAAAAF | 23a |
drc74/09/3 | Nsele * | 2009 | I | AAAAAAAAAAAAAAAAAAAAAAF | 23a |
drc74/09/4 | Nsele * | 2009 | I | AAAAAAAAAAAAAAAAAAAAAAF | 23a |
drc74/09/6 | Nsele * | 2009 | I | AAAAAAAAAAAAAAAAAAAAAAF | 23a |
drc94/09/2 | Kintambo * | 2009 | I | AAAAAAAAAAAAAAAAAAAAAAF | 23a |
drc27/11/3 | Ngafula * | 2011 | I | AAAAAAAAAAAAAAAAAAAAAAF | 23a |
drc27/11/5 | Ngafula * | 2011 | I | AAAAAAAAAAAAAAAAAAAAAAF | 23a |
drcKG28040802 | Kasavubu * | 2008 | I | AAAAAAAAAAAAAAAF | 16 |
drc96/12/1 | Mayanda | 2012 | I | AAAAAAAAAAAAAAAF | 16 |
drc96/12/2 | Mayanda | 2012 | I | AAAAAAAAAAAAAAAF | 16 |
drc96/12/3 | Mayanda | 2012 | I | AAAAAAAAAAAAAAAF | 16 |
drc99/05a | Ngafula * | 2005 | I | AAAAAAAAAAAAAF | 14 |
drc51/10/23 | Ndjili * | 2010 | I | AAAAAAAAAAAF | 12 |
drc85/10/13 | Ngafula * | 2010 | I | AAAAAAAAAAAF | 12 |
drc85/10/27 | Ngafula * | 2010 | I | AAAAAAAAAAAF | 12 |
drc86/10/3 | Ngafula * | 2010 | I | AAAAAAAAAAAF | 12 |
drc86/10/1 | Ngafula * | 2010 | I | AAAAAAAAAAAF | 12 |
drc108/10/1 | Ngafula * | 2010 | I | AAAAAAAAAAAF | 12 |
drc108/10/3 | Ngafula * | 2010 | I | AAAAAAAAAAAF | 12 |
drc108/10/5 | Ngafula * | 2010 | I | AAAAAAAAAAAF | 12 |
drc85/10/12 | Ngafula * | 2010 | I | AAAAAAAAAAF | 11 |
drc73/10/2 | Ngaliema * | 2010 | I | AAAAAAAAAAF | 11 |
drc73/10/3 | Ngaliema * | 2010 | I | AAAAAAAAAAF | 11 |
drc73/10/4 | Ngaliema * | 2010 | I | AAAAAAAAAAF | 11 |
drc49/05/P2a | Limete * | 2005 | I | AAAAAAAAAF | 10 |
drc85/10/25 | Ngafula * | 2010 | I | AAAAAAAAF | 9 |
drc75/05/1 | Maniema | 2005 | I | AAAAAAAAF | 9 |
drc49/05/p1b | Limete * | 2005 | I | AAAAAAAAF | 9 |
drc65/11/3 | Nsele * | 2011 | I | AAAAAAAF | 8 |
drc49/05/p1a | Limete * | 2005 | I | AAAAAF | 6 |
drc70/05/1 | Limete * | 2005 | I | AAAAF | 5 |
Con09/Ni16 | Congo 1 | 2009 | I | AAAAAAAAAF | 10 |
Kat67 | DRC(Zaire) 2 | 1967 | I | AAAAAAAABNABTDBNAAAAAAA | 23 |
Nig13_KAF_14 | Nigeria 3 | 2014 | I | ABNABNAAAAACBNAFA | 17 |
drc66/07/491 | Yakoma | 2007 | IX | AAABBAABBNABBAABBNABNABA | 24a |
drc66/07/43 | Yakoma | 2007 | IX | AAABNABBBNABBAABBNABNABA | 24b |
drc66/07/50 | Yakoma | 2007 | IX | AAABNABBBNABBAABBNABNABA | 24b |
drc66/07/492 | Yakoma | 2007 | IX | AAABNABBBNABBAABBNABNABA | 24b |
drc66/07/48 | Yakoma | 2007 | IX | AAAABNABBNABBAABBNABNABA | 24c |
drc35/08/p42 | Boende | 2008 | IX | AAAABNABBNABBAABBNABNABA | 24c |
drc35/08/18 | Boende | 2008 | IX | AAAABNABBNABBAABBNABNABA | 24c |
drc35/08/13 | Boende | 2008 | IX | AAAABNABBNABBAABBNABNABA | 24c |
drc35/08/3 | Boende | 2008 | IX | AAAABNABBNABBAABBNABNABA | 24c |
drc35/08/20 | Boende | 2008 | IX | AAAABNABBNABBAABBNABNABA | 24c |
drc35/08/1 | Boende | 2008 | IX | AAAABNABBNABBAABBNABNABA | 24c |
drc35/08/15 | Boende | 2008 | IX | AAAABNABBNABBAABBNABNABA | 24c |
drc35/08/3a | Boende | 2008 | IX | AAAABNABBNABBAABBNABNABA | 24c |
drc25/08/3 | Boende | 2008 | IX | AAAABNABBNABBAABBNABNABA | 24c |
drc25/08/9 | Boende | 2008 | IX | AAAABNABBNABBAABBNABNABA | 24c |
drc25/08/42 | Boende | 2008 | IX | AAAABNABBNABBAABBNABNABA | 24c |
drcKG31208/3 | Lingwala * | 2008 | IX | AAAABNABBNABBAAABNABNABA | 24d |
drc20/07/19 | Mahagi | 2007 | IX | AAABNABBNABBAABBNABNABA | 23b |
drc20/07/20 | Mahagi | 2007 | IX | AAABNABBNABBAABBNABNABA | 23b |
drc86/10/2 | Ngafula * | 2010 | IX | AAAAAAAAAAAF | 12 |
UG03H.1 | Uganda 4 | 2003 | IX | AAABNABBNABBAABBNABNABA | 23b |
Ken06.B1 | Kenya 5 | 2006 | IX | AAABNABBNABBAABBNABNABA | 23b |
drc35/10/3 | Ngaliema * | 2010 | XIV | AAAAAAAAAAAAAAAAAAAAAAAAAAAAABNABNBTDBN AAAAAAAAAAAF | 51 |
drc21/07/p22 | Kipushi | 2007 | XIV | AVVOVAVVNBVOV | 13 |
ETH/3 | Ethiopia 6 | 2011 | XXIII | ABNAAAAACBNABTDBNAFA | 20 |
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Mulumba–Mfumu, L.K.; Achenbach, J.E.; Mauldin, M.R.; Dixon, L.K.; Tshilenge, C.G.; Thiry, E.; Moreno, N.; Blanco, E.; Saegerman, C.; Lamien, C.E.; et al. Genetic Assessment of African Swine Fever Isolates Involved in Outbreaks in the Democratic Republic of Congo between 2005 and 2012 Reveals Co-Circulation of p72 Genotypes I, IX and XIV, Including 19 Variants. Viruses 2017, 9, 31. https://doi.org/10.3390/v9020031
Mulumba–Mfumu LK, Achenbach JE, Mauldin MR, Dixon LK, Tshilenge CG, Thiry E, Moreno N, Blanco E, Saegerman C, Lamien CE, et al. Genetic Assessment of African Swine Fever Isolates Involved in Outbreaks in the Democratic Republic of Congo between 2005 and 2012 Reveals Co-Circulation of p72 Genotypes I, IX and XIV, Including 19 Variants. Viruses. 2017; 9(2):31. https://doi.org/10.3390/v9020031
Chicago/Turabian StyleMulumba–Mfumu, Leopold K., Jenna E. Achenbach, Matthew R. Mauldin, Linda K. Dixon, Curé Georges Tshilenge, Etienne Thiry, Noelia Moreno, Esther Blanco, Claude Saegerman, Charles E. Lamien, and et al. 2017. "Genetic Assessment of African Swine Fever Isolates Involved in Outbreaks in the Democratic Republic of Congo between 2005 and 2012 Reveals Co-Circulation of p72 Genotypes I, IX and XIV, Including 19 Variants" Viruses 9, no. 2: 31. https://doi.org/10.3390/v9020031