Porcine circovirus-2 in Africa: Identification of continent-specific clusters and evidence of independent viral introductions from Europe, North America and Asia.
Africa
genotypes
phylogeographic analysis
porcine circovirus-2
Journal
Transboundary and emerging diseases
ISSN: 1865-1682
Titre abrégé: Transbound Emerg Dis
Pays: Germany
ID NLM: 101319538
Informations de publication
Date de publication:
Jul 2022
Jul 2022
Historique:
revised:
02
11
2021
received:
17
08
2021
accepted:
11
11
2021
pubmed:
24
11
2021
medline:
22
7
2022
entrez:
23
11
2021
Statut:
ppublish
Résumé
Porcine circovirus-2 (PCV-2) is associated with several disease syndromes in domestic pigs that have a significant impact on global pig production and health. Currently, little is known about the status of PCV-2 in Africa. In this study, a total of 408 archived DNA samples collected from pigs in Burkina Faso, Cameroon, Cape Verde, Ethiopia, the Democratic Republic of the Congo, Mozambique, Nigeria, Senegal, Tanzania and Zambia between 2000 and 2018 were screened by PCR for the presence of PCV-2. Positive amplicons of the gene encoding the viral capsid protein (ORF2) were sequenced to determine the genotypes circulating in each country. Four of the nine currently known genotypes of PCV-2 were identified (i.e. PCV-2a, PCV-2b, PCV-2d and PCV-2 g) with more than one genotype being identified in Burkina Faso, Ethiopia, Nigeria, Mozambique, Senegal and Zambia. Additionally, a phylogeographic analysis which included 38 additional ORF2 gene sequences of PCV-2s previously identified in Mozambique, Namibia and South Africa from 2014 to 2016 and 2019 to 2020 and available in public databases, demonstrated the existence of several African-specific clusters and estimated the approximate time of introduction of PCV-2s into Africa from other continents. This is the first in-depth study of PCV-2 in Africa and it has important implications for pig production at both the small-holder and commercial farm level on the continent.
Substances chimiques
DNA, Viral
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
e1142-e1152Informations de copyright
© 2021 Wiley-VCH GmbH.
Références
Achenbach, J. E., Gallardo, C., Nieto-Pelegrín, E., Rivera-Arroyo, B., Degefa-Negi, T., Arias, M., Jenberie, S., Mulisa, D. D., Gizaw, D., Gelaye, E., Chibssa, T. R., Belaye, A., Loitsch, A., Forsa, M., Yami, M., Diallo, A., Soler, A., Lamien, C. E., & Sánchez-Vizcaíno, J. M. (2017). Identification of a new genotype of African swine fever virus in domestic pigs from Ethiopia. Transboundary and Emerging Diseases, 64, 1393-1404.
Afolabi, K. O., Iweriebor, B. C., Obi, L. C., & Okoh, A. I. (2017). Molecular detection of porcine circovirus type 2 in swine herds of Eastern Cape Province South Africa. BMC Microbiology, 17, 1-10.
Alarcon, P., Rushton, J., & Wieland, B. (2013). Cost of post-weaning multi-systemic wasting syndrome and porcine circovirus type-2 subclinical infection in England - An economic disease model. Preventive Veterinary Medicine, 110, 88-102.
An, D. J., Roh, I. S., Song, D. S., Park, C. K., & Park, B. K. (2007). Phylogenetic characterization of porcine circovirus type 2 in PMWS and PDNS Korean pigs between 1999 and 2006. Virus Research, 129, 115-122.
Baele, G., Lemey, P., Bedford, T., Rambaut, A., Suchard, M. A., & Alekseyenko, A. V. (2012). Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty. Molecular Biology and Evolution, 29, 2157-2167.
Chang'a, J. S., Mayenga, C., Settypalli, T. B. K., Achenbach, J. E., Mwanandota, J. J., Magidanga, B., Cattoli, G., Jeremiah, M., Kamigwe, A., Guo, S., Kalabi, D., Mramba, F., & Lamien, C. E. (2019). Symptomatic and asymptomatic cases of African swine fever in Tanzania. Transboundary and Emerging Diseases, 66, 2402-2410.
Choi, C.-Y., Choi, Y.-C., Park, I.-B., Lee, C.-H., Kang, S.-J., & Chun, T. (2018). The ORF5 protein of porcine circovirus type 2 enhances viral replication by dampening type I interferon expression in porcine epithelial cells. Veterinary Microbiology, 226, 50-58.
Cortey, M., Pileri, E., Sibila, M., Pujols, J., Balasch, M., Plana, J., & Segalés, J. (2011). Genotypic shift of porcine circovirus type 2 from PCV-2a to PCV-2b in Spain from 1985 to 2008. Veterinary Journal, 187, 363-368.
Darriba, D., Taboada, G. L., Doallo, R., & Posada, D. (2012). JModelTest 2: More models, new heuristics and parallel computing. Nature Methods, 9, 772.
Drummond, A. J., Ho, S. Y. W. W., Phillips, M. J., & Rambaut, A. (2006). Relaxed phylogenetics and dating with confidence. PLoS Biology, 4, e88.
Dupont, K., Nielsen, E. O., Baekbo, P., & Larsen, L. E. (2008). Genomic analysis of PCV2 isolates from Danish archives and a current PMWS case-control study supports a shift in genotypes with time. Veterinary Microbiology, 128, 56-64.
Dvorak, C. M. T., Yang, Y., Haley, C., Sharma, N., & Murtaugh, M. P. (2016). National reduction in porcine circovirus type 2 prevalence following introduction of vaccination. Veterinary Microbiology, 189, 86-90.
Eleazar, A. N., Takeet, M. I., Sonibare, A. O., Olufemi, F. O., & Otesile, E. B. (2020). Prevalence of porcine circovirus type 2 in naturally infected pigs in Abeokuta, Nigeria. Folia Veterinaria, 64, 29-37.
Finsterbusch, T., & Mankertz, A. (2009). Porcine circoviruses - Small but powerful. Virus Research, 143, 177-183.
Firth, C., Charleston, M. A., Duffy, S., Shapiro, B., & Holmes, E. C. (2009). Insights into the evolutionary history of an emerging livestock pathogen: Porcine circovirus 2. Journal of Virology, 83, 12813-12821.
Franzo, G., Tucciarone, C. M., Dotto, G., Gigli, A., Ceglie, L., & Drigo, M. (2015a). International trades, local spread and viral evolution: The case of porcine circovirus type 2 (PCV2) strains heterogeneity in Italy. Infection, Genetics and Evolution, 32, 409-415.
Franzo, G., Cortey, M., Martins Gomes de Castro, A. M., Piovezan, U., Szabo, M. P. J., Drigo, M., Segalés, J., & Richtzenhain, L. J. (2015b) Genetic characterisation of porcine circovirus type 2 (pcv2) strains from feral pigs in the Brazilian Pantanal: An opportunity to reconstruct the history of PCV2 evolution. Veterinary Microbiology, 178, 158-162.
Franzo, G., Cortey, M., Segalés, J., Hughes, J., & Drigo, M. (2016). Phylodynamic analysis of porcine circovirus type 2 reveals global waves of emerging genotypes and the circulation of recombinant forms. Molecular Phylogenetics and Evolution, 100, 269-280.
Franzo, G., & Segalés, J. (2018). Porcine circovirus 2 (PCV-2) genotype update and proposal of a new genotyping methodology. Plos One, 13, e0208585.
Franzo, G., & Segalés, J. (2020a). Circoviruses (Circoviridae). In D.H. Bamford & M. Zuckerman (Eds.), Encyclopedia of virology (pp. 182-192). Elsevier Science, ISBN 9780128145166.
Franzo, G., & Segalés, J. (2020b). Porcine circovirus 2 genotypes, immunity and vaccines: Multiple genotypes but one single serotype. Pathogens, 9, 1-12.
Franzo, G., Tinello, S., Grassi, L., Tucciarone, C. M., Legnardi, M., Cecchinato, M., Dotto, G., Mondin, A., Martini, M., Pasotto, D., Menandro, M. L., & Drigo, M. (2020). Free to circulate: An update on the epidemiological dynamics of porcine circovirus 2 (PCV-2) in Italy reveals the role of local spreading, wild populations, and foreign countries. Pathogens, 9, 221.
Gao, Z., Dong, Q., Jiang, Y., Opriessnig, T., Wang, J., Quan, Y., & Yang, Z. (2014). ORF4-protein deficient PCV2 mutants enhance virus-induced apoptosis and show differential expression of mRNAs in vitro. Virus Research, 183, 56-62.
Ge, X., Wang, F., Guo, X., & Yang, H. (2012). Porcine circovirus type 2 and its associated diseases in China. Virus Research, 164, 100-106.
Ginestet, C. (2011). Ggplot2: Elegant graphics for data analysis. Journal of the Royal Statistical Society: Series A (Statistics in Society), 174, 245-246.
Guindon, S., Dufayard, J. F., Lefort, V., Anisimova, M., Hordijk, W., & Gascuel, O. (2010). New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0. Systematic Biology, 59, 307-321.
Hill, V., & Baele, G. (2019). Bayesian estimation of past population dynamics in BEAST 1.10 using the Skygrid coalescent model. Molecular Biology and Evolution, 36, 2620-2628.
Juhan, N. M., LeRoith, T., Opriessnig, T., & Meng, X. J. (2009). The open reading frame 3 (ORF3) of porcine circovirus type 2 (PCV2) is dispensable for virus infection but evidence of reduced pathogenicity is limited in pigs infected by an ORF3-null PCV2 mutant. Virus Research, 147, 60-66.
Laisse, C. J., Souza, C. K., Pereira, P. R., de Lorenzo, C., Bianchi, M. V., Mapaco, L. P., Pavarini, S. P., Canal, C. W., & Driemeier, D. (2018). Detection and phylogenetic characterization of porcine circovirus 2 from pigs in Mozambique. Journal of Veterinary Diagnostic Investigation, 30, 342-347.
Lemey, P., Rambaut, A., Drummond, A. J., & Suchard, M. A. (2009). Bayesian phylogeography finds its roots. PLoS Computational Biology, 5, e1000520.
Luka, P. D., Achenbach, J. E., Mwiine, F. N., Lamien, C. E., Shamaki, D., Unger, H., & Erume, J. (2017). Genetic characterization of circulating african swine fever viruses in Nigeria (2007-2015). Transboundary and Emerging Diseases, 6, 1598-1609.
Li, D., Wang, J., Xu, S., Cai, S., Ao, C., Fang, L., Xiao, S., Chen, H., & Jiang, Y. (2018). Identification and functional analysis of the novel ORF6 protein of porcine circovirus type 2 in vitro. Veterinary Research Communications, 42, 1-10.
Martin, D. P., Murrell, B., Golden, M., Khoosal, A., & Muhire, B. (2015). RDP4: Detection and analysis of recombination patterns in virus genomes. Virus Evolution, 1(1), vev003.
Minoungou, G. L., Diop, M., Dakouo, M., Ouattara, A. K., Settypalli, T. B. K., Lo, M. M., Sidibe, S., Kanyala, E., Kone, Y. S., Diallo, M. S., Ouedraogo, A., Coulibaly, K., Ouedraogo, V., Sow, I., Niang, M., Achenbach, J. E., Wade, A., Unger, H., Diallo, A., …Simpore, J. (2021). Molecular characterization of African Swine fever viruses in Burkina Faso, Mali, and Senegal 1989-2016: Genetic diversity of ASFV in West Africa. Transboundary and Emerging Diseases, 68, 2842-2852.
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., & Diallo, A. (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, 31.
Molini, U., Franzo, G., Gous, L., Moller, S., Hemberger, Y. M., Chiwome, B., Marruchella, G., Khaiseb, S., Cattoli, G., & Dundon, W. G. (2021). Three different genotypes of porcine circovirus 2 (PCV-2) identified in pigs and warthogs in Namibia. Archives of Virology, 166, 1723-1728.
Nguyen, L. T., Schmidt, H. A., von Haeseler, A., & Minh, B. Q. (2015). IQ-TREE: A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Molecular Biology and Evolution, 32, 268-274.
R Core Team. (2021). R: A language and environment for statistical computing. Vienna: R Foundation for Statistical Computing, Austria. URL https://www.R-project.org/
Reiner, G., Hofmeister, R., & Willems, H. (2015). Genetic variability of porcine circovirus 2 (PCV2) field isolates from vaccinated and non-vaccinated pig herds in Germany. Veterinary Microbiology, 180, 41-48.
Segalés, J. (2012). Porcine circovirus type 2 (PCV2) infections: Clinical signs, pathology and laboratory diagnosis. Virus Research, 164, 10-19.
Shen, H. G., Halbur, P. G., & Opriessnig, T. (2012). Prevalence and phylogenetic analysis of the current porcine circovirus 2 genotypes after implementation of widespread vaccination programmes in the USA. Journal of General Virology, 93, 1345-1355.
Standley, K. (2013). MAFFT multiple sequence alignment software version 7: Improvements in performance and usability (Outlines Version 7). Molecular Biology and Evolution, 30, 772-780.
Suchard, M. A., Lemey, P., Baele, G., Ayres, D. L., Drummond, A. J., & Rambaut, A. (2018). Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10. Virus Evolution, 4, vey016.
Vidigal, P. M. P., Mafra, C. L., Silva, F. M. F., Fietto, J. L. R., Silva Júnior, A., & Almeida, M. R. (2012). Tripping over emerging pathogens around the world: A phylogeographical approach for determining the epidemiology of porcine circovirus-2 (PCV-2), considering global trading. Virus Research, 163, 320-327.
Wade, A., Achenbach, J. E., Gallardo, C., Settypalli, T. B. K., Souley, A., Djonwe, G., Loitsch, A., Dauphin, G., Ngang, J. J. E., Boyomo, O., Cattoli, G., Diallo, A., & Lamien, C. E. (2019). Genetic characterization of African swine fever virus in Cameroon, 2010-2018. Journal of Microbiology, 57, 316-324.
Wang, Y., Noll, L., Lu, N., Porter, E., Stoy, C., Zheng, W., Liu, X., Peddireddi, L., Niederwerder, M., & Bai, J. (2020). Genetic diversity and prevalence of porcine circovirus type 3 (PCV3) and type 2 (PCV2) in the midwest of the USA during 2016-2018. Transboundary and Emerging Diseases, 67, 1284-1294.
Xiao, C. T., Halbur, P. G., & Opriessnig, T. (2015). Global molecular genetic analysis of porcine circovirus type 2 (PCV2) sequences confirms the presence of four main PCV2 genotypes and reveals a rapid increase of PCV2d. Journal of General Virology, 96, 1830-1841.
Yu, G., Smith, D. K., Zhu, H., Guan, Y., & Lam, T. T. Y. (2017). Ggtree: An r package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution, 8, 28-36.
Zhai, S. -L., Lu, S. -S., Wei, W.-K., Lv, D. -H., Wen, X. -H., Zhai, Q., Chen, Q. -L., Sun, Y.-W., & Xi, Y. (2019). Reservoirs of porcine circoviruses: A mini review. Frontiers in Veterinary Science, 6, 319.