A Novel Terrestrial Rabies Virus Lineage Occurring in South America: Origin, Diversification, and Evidence of Contact between Wild and Domestic Cycles
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sample Acquisition and Sequencing
2.2. Bayesian Phylogenetic Analysis of Dog-Related Variants
2.3. Phylogeographic Analysis of AgV2
2.4. Temporal Analysis
2.5. Network Analysis
2.6. Ancestral States Reconstruction
2.7. Recombination Analysis
2.8. Selection Analysis
2.9. Amino Acid Ancestral Reconstruction
3. Results
3.1. Phylogenetic Analysis and Origins of the AgV2 Lineage
3.2. Phylogeographic Analysis
3.3. Cross-Species Transmission Analysis
3.4. Recombination Analysis
3.5. Selection Analysis
3.6. Amino Acid Replacements
4. Discussion
4.1. Origins and Diversification of AgV2
4.2. Cross-Species Transmission
4.3. Host Shifting and Adaptation
4.4. Interaction between Domestic and Wild Cycles
4.5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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No. | Species | Country | Province | Locality | Year | Variant | Genbank Accession Number |
---|---|---|---|---|---|---|---|
AA35 | Dog | Argentina | Tucumán | Concepción | 1995 | AgV2 | OL451878 |
AA38 | Dog | Argentina | Tucumán | Aguilares | 1996 | AgV2 | OL451879 |
AA39 | Dog | Argentina | Tucumán | Chicligasta | 1996 | AgV2 | OL451880 |
552 | C. thous | Argentina | Chaco | El Espinillo | 1997 | AgV2 | OL451910 |
AA53 | Dog | Argentina | Formosa | Pozo del Tigre | 2000 | AgV2 | OL451881 |
AA71 | Dog | Argentina | Formosa | Pirané | 2000 | AgV2 | OL451882 |
AA112 | Dog | Argentina | Chaco | Ciervo Petizo | 2001 | AgV2 | OL451883 |
AA120 | Dog | Argentina | Chaco | Pampa Almirón | 2001 | AgV2 | OL451884 |
A119 | C. thous | Argentina | Chaco | Pampa Almirón | 2001 | AgV2 | OL451912 |
A166 | Dog | Argentina | Formosa | Potrero Norte | 2002 | AgV2 | OL451909 |
AA148 | Dog | Argentina | Chaco | Pirané | 2002 | AgV2 | OL451913 |
AA474 | C. thous | Argentina | Chaco | Presidencia Roca | 2004 | AgV2 | OL451885 |
A696 | C. thous | Argentina | Chaco | Resistencia | 2006 | AgV2 | OL451911 |
AA774 | Dog | Argentina | Formosa | Gran Guardia | 2007 | AgV2 | OL451886 |
AA881 | Dog | Argentina | Formosa | Palo Santo | 2007 | AgV2 | OL451914 |
AA886 | C. thous | Argentina | Formosa | Colonia Da Prato | 2008 | AgV2 | OL451887 |
AA888 | Dog | Argentina | Formosa | NA | 2008 | AgV2 | OL451888 |
AA911 | Dog | Argentina | Chaco | Pampa del Indio | 2008 | AgV2 | OL451889 |
A874 | Dog | Argentina | Chaco | Capitán Solari | 2008 | AgV2 | OL451906 |
AA929 | N. nasua | Argentina | Chaco | Laguna Limpia | 2009 | AgV2 | OL451890 |
AA957 | Dog | Argentina | Chaco | Colonia Elisa | 2009 | AgV2 | OL451891 |
AA959 | Dog | Argentina | Chaco | Colonia Elisa | 2009 | AgV2 | OL451892 |
AA966 | N. nasua | Argentina | Formosa | Palo Santo | 2009 | AgV2 | OL451893 |
AB124 | Dog | Argentina | Formosa | Comandante Fontana | 2012 | AgV2 | OL451894 |
AB160 | Dog | Argentina | Formosa | Ibarreta | 2013 | AgV2 | OL451895 |
AB193 | C. thous | Argentina | Chaco | La Verde | 2013 | AgV2 | OL451896 |
AB353 | Dog | Argentina | Formosa | Ibarreta | 2013 | AgV2 | OL451897 |
AB356 | C. thous | Argentina | Formosa | El Colorado | 2013 | AgV2 | OL451898 |
AB357 | Dog | Argentina | Formosa | Laishi | 2013 | AgV2 | OL451899 |
AB361 | N. nasua | Argentina | Formosa | Mariano Boedo | 2013 | AgV2 | OL451900 |
AB362 | Dog | Argentina | Formosa | Comandante Fontana | 2013 | AgV2 | OL451901 |
AB118 | Dog | Argentina | Formosa | S/D | 2015 | AgV2 | OL451902 |
AB122 | Dog | Argentina | Chaco | Puerto Tirol | 2015 | AgV2 | OL451903 |
739 | Dog | Argentina | Chaco | Pampa Almirón | 2016 | AgV2 | OL451904 |
682 | Dog | Argentina | Chaco | Laguna Blanca | 2017 | AgV2 | OL451905 |
257 | Dog | Brazil | Mato Grosso do Sul | Pantanais | 1989 | AgV2 | OL451915 |
352 | Dog | Paraguay | Itapúa | Encarnación | 1991 | AgV2 | OL451908 |
353 | Dog | Paraguay | Itapúa | Encarnación | 1991 | AgV2 | OL451916 |
369 | Dog | Paraguay | Itapúa | Encarnación | 1992 | AgV2 | OL451907 |
AA42 | Dog | Argentina | Salta | Orán | 1999 | AgV1 | OL451918 |
AA47 | Cat | Argentina | Salta | Orán | 1999 | AgV1 | OL451919 |
AA50 | Cat | Argentina | Salta | Orán | 1999 | AgV1 | OL451920 |
AA21 | Dog | Argentina | Salta | Hipólito Yrigoyen | 2000 | AgV1 | OL451917 |
AA126 | Dog | Argentina | Salta | NA | 2002 | AgV1 | OL451921 |
AA178 | Dog | Argentina | Salta | Aguaray | 2002 | AgV1 | OL451922 |
AA180 | Monkey | Argentina | Salta | Tartagal | 2002 | AgV1 | OL451923 |
AA183 | Dog | Argentina | Salta | Tartagal | 2002 | AgV1 | OL451924 |
M863 | Dog | Argentina | Jujuy | Palpalá | 2003 | AgV1 | OL451929 |
M870 | Dog | Argentina | Jujuy | El Carmen | 2003 | AgV1 | OL451930 |
M1009 | Dog | Argentina | Jujuy | S.S. de Jujuy | 2003 | AgV1 | OL451932 |
M632 | Dog | Argentina | Jujuy | S.S. de Jujuy | 2005 | AgV1 | OL451926 |
M654 | Dog | Argentina | Jujuy | S.S. de Jujuy | 2005 | AgV1 | OL451928 |
M639 | Dog | Argentina | Jujuy | S.S. de Jujuy | 2006 | AgV1 | OL451927 |
M876 | Dog | Argentina | Jujuy | S.S. de Jujuy | 2006 | AgV1 | OL451931 |
M297 | Dog | Argentina | Salta | Orán | 2015 | AgV1 | OL451925 |
(a) Site-Based Methods | |||||
---|---|---|---|---|---|
Length (Codons) | Type of Selection | FEL | SLAC | FUBAR | MEME |
450 | Positive | 2 | 0 | 0 | 3 |
Negative | 193 | 162 | 311 | - | |
Codons | 77,339 | - | - | 158, 419, 443 | |
(b) Branch-Based Methods | |||||
Method | Test Group | Reference Group | Result | ||
aBSREL | All AgV2 | - | No EDS (p ≤ 0.05) | ||
aBSREL | AM3b MRCA + Brazilian Wild A + B MRCA | - | No EDS (p ≤ 0.05) | ||
aBSREL | AM3b MRCA + Brazilian Wild A + B | - | No EDS (p = 0.0057 ≤ 0.05) | ||
Relax | AM3b MRCA + Brazilian Wild A + B | All remaining branches | Selection Relaxation not significant (K = 0.94, p = 0.360, LR = 0.84) | ||
BUSTED | AM3b MRCA + Brazilian Wild A + B | All remaining branches | Evidence of gene-wide EDS (LRT, p-value = 0.022 ≤ 0.05) |
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Caraballo, D.A.; Lema, C.; Novaro, L.; Gury-Dohmen, F.; Russo, S.; Beltrán, F.J.; Palacios, G.; Cisterna, D.M. A Novel Terrestrial Rabies Virus Lineage Occurring in South America: Origin, Diversification, and Evidence of Contact between Wild and Domestic Cycles. Viruses 2021, 13, 2484. https://doi.org/10.3390/v13122484
Caraballo DA, Lema C, Novaro L, Gury-Dohmen F, Russo S, Beltrán FJ, Palacios G, Cisterna DM. A Novel Terrestrial Rabies Virus Lineage Occurring in South America: Origin, Diversification, and Evidence of Contact between Wild and Domestic Cycles. Viruses. 2021; 13(12):2484. https://doi.org/10.3390/v13122484
Chicago/Turabian StyleCaraballo, Diego A., Cristina Lema, Laura Novaro, Federico Gury-Dohmen, Susana Russo, Fernando J. Beltrán, Gustavo Palacios, and Daniel M. Cisterna. 2021. "A Novel Terrestrial Rabies Virus Lineage Occurring in South America: Origin, Diversification, and Evidence of Contact between Wild and Domestic Cycles" Viruses 13, no. 12: 2484. https://doi.org/10.3390/v13122484