WHOLE GENOME SEQUENCING AND GENOTYPING PROTOCOL OF RABIES VIRUS ISOLATES
Main Article Content
Authors
G. Yessembekova
S. Seifullin Kazakh AgroTechnical University, Zhenis avenue, 62, Kazakhstan, Astana, 010011
A. Abenova
S. Seifullin Kazakh AgroTechnical University, Zhenis avenue, 62, Kazakhstan, Astana, 010011
A. Amirgazin
National Center for Biotechnology, 13/5, Korgalzhyn road, Kazakhstan, Nur-Sultan, 010000
T. Karibayev
National Center for Biotechnology, 13/5, Korgalzhyn road, Kazakhstan, Nur-Sultan, 010000
A. Shevtsov
National Center for Biotechnology, 13/5, Korgalzhyn road, Kazakhstan, Nur-Sultan, 010000
S. Abdrakhmanov
National Center for Biotechnology, 13/5, Korgalzhyn road, Kazakhstan, Nur-Sultan, 010000
Abstract
This study describes the developed protocol for whole genome sequencing of clinical Rabies virus RNA samples on the Illumina MiSeq platform. Previously, genotyping of the rabies virus circulating in Kazakhstan was based on the nucleoprotein gene sequence (N gene). The protocol describes the methods of sample preparation, whole genome sequencing and genotyping currently used for epidemiological analysis not only of Rabies virus, but also for other viral pathogens such as SARS-CoV-2, Influenza and others. The aim of the work was to develop and test a protocol for whole genome sequencing and genetyping of rabies virus isolates for further use in epidemiological monitoring. As a result of the research, whole genome sequences of 31 isolates of Rabies virus isolated from various infected animals and regions of Kazakhstan were obtained for the first time. All the isolates belong to the major steppe-type clade – Cosmopolitan (30 isolates belong to the minor clade CA1, while 1 isolate belongs to an unassigned minor clade). 2 local outbreaks and 6 separated rabies virus lineages were identified. Estimated dates of divergence from a common ancestor were calculated for both the Cosmopolitan clade and the minor clade CA1.
Keywords
Rabies, epidemiology, sequencing, outbreak
Article Details
References
Wunner W. H., Jackson A. C. Rabies: scientific basis of the disease and its management // Elsevier Science. ‒ 2010. Vol. 4, № 4. ‒ P. 43‒44. ISBN: 0080550096
Troupin C., Dacheux L., Tanguy M., Sabeta C., Blanc H., Bouchier C., Vignuzzi M., Duchene S., Holmes E. C., Bourhy H. Large-scale phylogenomic analysis reveals the complex evolutionary history of rabies virus in multiple carnivore hosts // PLoS pathogens. ‒ 2016. ‒ Vol. 12, № 12. ‒ P. e1006041 Crossref
Kuzmin I. V., Botvinkin A. D., McElhinney L. M., Smith J. S., Orciari L. A., Hughes G. J., Fooks A. R., Rupprecht C. E. Molecular epidemiology of terrestrial rabies in the former Soviet Union // Journal of wildlife diseases. ‒ 2004. ‒ Vol. 40, № 4. ‒ P. 617‒631. Crossref
Abdrakhmanov S. K., Beisembayev K. K., Korennoy F. I., Yessembekova G. N., Kushubaev D. B., Kadyrov A. S. Revealing spatio-temporal patterns of rabies spread among various categories of animals in the Republic of Kazakhstan, 2010-2013 // Geospatial Health. ‒ 2016. ‒ Vol. 11:455, № 2. ‒ P. 199‒205. Crossref
Sultanov A. A., Abdrakhmanov S. K., Abdybekova A. M., Karatayev B. S., Torgerson P. R. Rabies in Kazakhstan // PLoS neglected tropical diseases. ‒ 2016. ‒ Vol. 10, № 8. ‒ P. e0004889. Crossref
Rupprecht C. E., Fooks A. R., Abela-Ridder B. Laboratory techniques in rabies // World Health Organization. ‒ 2018. ‒ Vol 1. № 5. ‒ P. 289. URL
Deviatkin A. A., Lukashev A. N., Poleshchuk E. M., Dedkov V. G., Tkachev S. E., Sidorov G. N., Karganova G. G., Galkina I. V., Shchelkanov M. Y., Shipulin G. A. The phylodynamics of the rabies virus in the Russian Federation // PLoS One. ‒ 2017. ‒ Vol. 12, № 2. ‒ P. e0171855. Crossref
Pimentel M. F. A., Nassarden S. M., Cândido S. L., Dutra V., Nakazato L. Genotyping of rabies positive samples isolated from animals in Mato Grosso and Rondônia–Brazil // Infection, Genetics and Evolution. ‒ 2022. ‒ Vol. 103. ‒ P. 105336. Crossref
Calvelage S., Freuling C. M., Fooks A. R., Höper D., Marston D. A., McElhinney L., Rasmussen T. B., Finke S., Beer M., Müller T. Full-genome sequences and phylogenetic analysis of archived Danish European bat lyssavirus 1 (EBLV-1) emphasize a higher genetic resolution and spatial segregation for sublineage 1a // Viruses. ‒ 2021. ‒ Vol. 13, № 4. ‒ P. 634. Crossref
Hu S.C., Hsu C.L., Lee M.S., Tu Y.C., Chang J.C., Wu C.H., Lee S.H., Ting L.J., Tsai K.R., Cheng M.C. Lyssavirus in Japanese Pipistrelle, Taiwan // Emerging Infectious Diseases. ‒ 2018. ‒ Vol. 24, № 4. ‒ P. 782. Crossref PMID: 29553328
Al-Eitan L. N., Wu G., Golding M., Tang Y., Goharriz H., Marston D. A., Fooks A. R., McElhinney L. M. Whole-genome sequencing and phylogenetic analysis of rabies viruses from Jordan // PLoS neglected tropical diseases. ‒ 2021. ‒ Vol. 15, № 5. ‒ P. e0009431. Crossref
Hyeon J.-Y., Risatti G. R., Helal Z. H., McGinnis H., Sims M., Hunt A., Chung D. H., Kim J., Desiato J., Lee D.H. Whole Genome Sequencing and Phylogenetic Analysis of Rabies Viruses from Bats in Connecticut, USA, 2018–2019 // Viruses. ‒ 2021. ‒ Vol. 13, № 12. ‒ P. 2500. Crossref
Bacus M. G., Buenaventura S. G. C., Mamites A. M. C., Elizagaque H. G., Labrador C. C., Delfin F. C., Eng M. N. J., Lagare A. P., Marquez G. N., Murao L. A. E. Genome-based local dynamics of canine rabies virus epidemiology, transmission, and evolution in Davao City, Philippines, 2018–2019 // Infection, Genetics and Evolution. ‒ 2021. ‒ Vol. 92. ‒ P. 104868. Crossref
Forró B., Marton S., Fehér E., Domán M., Kemenesi G., Cadar D., Hornyák Á., Bányai K. Phylogeny of Hungarian EBLV‐1 strains using whole‐genome sequence data // Transboundary and Emerging Diseases. ‒ 2021. ‒ Vol. 68, № 3. ‒ P. 1323-1331. Crossref
Zhang Y., Vrancken B., Feng Y., Dellicour S., Yang Q., Yang W., Zhang Y., Dong L., Pybus O. G., Zhang H. Cross-border spread, lineage displacement and evolutionary rate estimation of rabies virus in Yunnan Province, China // Virology journal. ‒ 2017. ‒ Vol. 14, № 1. ‒ P. 1-8. Crossref
Feng Y., Wang W., Guo J., Li Y., Yang G., Su N., Zhang L., Xu W., Sheng Z., Ma L. Disease outbreaks caused by steppe-type rabies viruses in China // Epidemiology & Infection. ‒ 2015. ‒ Vol. 143, № 6. ‒ P. 1287-1291. Crossref
Poleshchuk E., Deviatkin A., Dedkov V., Sidorov G., Ochkasova J., Hodjakova I., Schukina I., Savel'ev S., Golenskih A., Shipulin G. Complete genome sequences of four virulent rabies virus strains isolated from rabid animals in Russia // Genome announcements. ‒ 2013. ‒ Vol. 1, № 3. ‒ P. e00140-13. Crossref
Hao L., Guo Z. Y., Zhang J., Tao X. Y., Zhu W. Y., Qing T., Liu H. T. Whole Genome Sequencing and Comparisons of Different Chinese Rabies Virus Lineages Including the First Complete Genome of an Arctic-like Strain in China // Biomedical and Environmental Sciences. ‒ 2016. ‒ Vol. 29, № 5. ‒ P. 340-346. Crossref