Display options
Cite
Brunker K, Jaswant G, Thumbi SM, et al. Rapid in-country sequencing of whole virus genomes to inform rabies elimination programmes. Wellcome Open Res. 2020;5:3doi: 10.12688/wellcomeopenres.15518.1.
Brunker, K., Jaswant, G., Thumbi, S. M., Lushasi, K., Lugelo, A., Czupryna, A. M., Ade, F., Wambura, G., Chuchu, V., Steenson, R., Ngeleja, C., Bautista, C., Manalo, D. L., Gomez, M. R. R., Chu, M. Y. J. V., Miranda, M. E., Kamat, M., Rysava, K., Espineda, J., Silo, E. A. V., Aringo, A. M., Bernales, R. P., Adonay, F. F., Tildesley, M. J., Marston, D. A., Jennings, D. L., Fooks, A. R., Zhu, W., Meredith, L. W., Hill, S. C., Poplawski, R., Gifford, R. J., Singer, J. B., Maturi, M., Mwatondo, A., Biek, R., & Hampson, K. (2020). Rapid in-country sequencing of whole virus genomes to inform rabies elimination programmes. Wellcome open research, 53. https://doi.org/10.12688/wellcomeopenres.15518.1
Brunker, Kirstyn, et al. "Rapid in-country sequencing of whole virus genomes to inform rabies elimination programmes." Wellcome open research vol. 5 (2020): 3. doi: https://doi.org/10.12688/wellcomeopenres.15518.1
Brunker K, Jaswant G, Thumbi SM, Lushasi K, Lugelo A, Czupryna AM, Ade F, Wambura G, Chuchu V, Steenson R, Ngeleja C, Bautista C, Manalo DL, Gomez MRR, Chu MYJV, Miranda ME, Kamat M, Rysava K, Espineda J, Silo EAV, Aringo AM, Bernales RP, Adonay FF, Tildesley MJ, Marston DA, Jennings DL, Fooks AR, Zhu W, Meredith LW, Hill SC, Poplawski R, Gifford RJ, Singer JB, Maturi M, Mwatondo A, Biek R, Hampson K. Rapid in-country sequencing of whole virus genomes to inform rabies elimination programmes. Wellcome Open Res. 2020 Jan 07;5:3. doi: 10.12688/wellcomeopenres.15518.1. eCollection 2020. PMID: 32090172; PMCID: PMC7001756.
Copy Download .nbib Format: NLM
Share it on

Wellcome Open Res. 2020 Jan 07;5:3. doi: 10.12688/wellcomeopenres.15518.1. eCollection 2020.

Rapid in-country sequencing of whole virus genomes to inform rabies elimination programmes.

Wellcome open research

Kirstyn Brunker, Gurdeep Jaswant, S M Thumbi, Kennedy Lushasi, Ahmed Lugelo, Anna M Czupryna, Fred Ade, Gati Wambura, Veronicah Chuchu, Rachel Steenson, Chanasa Ngeleja, Criselda Bautista, Daria L Manalo, Ma Ricci R Gomez, Maria Yna Joyce V Chu, Mary Elizabeth Miranda, Maya Kamat, Kristyna Rysava, Jason Espineda, Eva Angelica V Silo, Ariane Mae Aringo, Rona P Bernales, Florencio F Adonay, Michael J Tildesley, Denise A Marston, Daisy L Jennings, Anthony R Fooks, Wenlong Zhu, Luke W Meredith, Sarah C Hill, Radoslaw Poplawski, Robert J Gifford, Joshua B Singer, Mathew Maturi, Athman Mwatondo, Roman Biek, Katie Hampson

Affiliations

  1. Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK.
  2. The Boyd Orr Centre for Population and Ecosystem Health, University of Glasgow, Glasgow, G12 8QQ, UK.
  3. University of Nairobi Institute of Tropical and Infectious Diseases (UNITID), Nairobi, Kenya.
  4. Center for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya.
  5. Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, USA.
  6. Ifakara Health Institute, Ifakara, Tanzania.
  7. Department of Veterinary Medicine and Public Health, Sokoine University of Agriculture, Morogoro, Tanzania.
  8. Tanzania Veterinary Laboratory Agency, Ministry of Livestock and Fisheries Development, Dar es Salaam, Tanzania.
  9. Research Institute for Tropical Medicine (RITM), Manilla, Philippines.
  10. Field Epidemiology Training Program Alumni Foundation (FETPAFI), Manilla, Philippines.
  11. The Zeeman Institute for Systems Biology & Infectious Disease Epidemiology Research, School of Life Sciences and Mathematical Institute, University of Warwick, Coventry, UK.
  12. Department of Agriculture Regional Field Office 5, Regional Animal Disease, Diagnostic Laboratory, Cabangan, Camalig, Albay, Philippines.
  13. Albay Veterinary Office, Provincial Government of Albay, Albay Farmers' Bounty Village, Cabangan, Camalig, Albay, Philippines.
  14. Wildlife Zoonoses & Vector-Borne Diseases Research Group, Animal and Plant Health Agency (APHA), Weybridge, UK.
  15. Institute of Infection and Global Health,, University of Liverpool, Liverpool, UK.
  16. Department of Pathology, University of Cambridge, Cambridge, UK.
  17. University of Oxford, Oxford, UK.
  18. Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK.
  19. Advanced Research Computing, University of Birmingham, Birmingham, B15 2TT, UK.
  20. MRC-University of Glasgow Centre for Virus Research (CVR), University of Glasgow, Glasgow, UK.
  21. Zoonotic Disease Unit, Ministry of Health, Ministry of Agriculture, Livestock and Fisheries, Nairobi, Kenya.

PMID: 32090172 PMCID: PMC7001756 DOI: 10.12688/wellcomeopenres.15518.1

Abstract

Genomic surveillance is an important aspect of contemporary disease management but has yet to be used routinely to monitor endemic disease transmission and control in low- and middle-income countries. Rabies is an almost invariably fatal viral disease that causes a large public health and economic burden in Asia and Africa, despite being entirely vaccine preventable. With policy efforts now directed towards achieving a global goal of zero dog-mediated human rabies deaths by 2030, establishing effective surveillance tools is critical. Genomic data can provide important and unique insights into rabies spread and persistence that can direct control efforts. However, capacity for genomic research in low- and middle-income countries is held back by limited laboratory infrastructure, cost, supply chains and other logistical challenges. Here we present and validate an end-to-end workflow to facilitate affordable whole genome sequencing for rabies surveillance utilising nanopore technology. We used this workflow in Kenya, Tanzania and the Philippines to generate rabies virus genomes in two to three days, reducing costs to approximately £60 per genome. This is over half the cost of metagenomic sequencing previously conducted for Tanzanian samples, which involved exporting samples to the UK and a three- to six-month lag time. Ongoing optimization of workflows are likely to reduce these costs further. We also present tools to support routine whole genome sequencing and interpretation for genomic surveillance. Moreover, combined with training workshops to empower scientists in-country, we show that local sequencing capacity can be readily established and sustainable, negating the common misperception that cutting-edge genomic research can only be conducted in high resource laboratories. More generally, we argue that the capacity to harness genomic data is a game-changer for endemic disease surveillance and should precipitate a new wave of researchers from low- and middle-income countries.

Copyright: © 2020 Brunker K et al.

Keywords: MinION; dog-mediated rabies; field sequencing; lyssavirus; nanopore; neglected tropical diseases; phylogenetic; rabies virus; surveillance; whole genome sequencing; zoonoses

Conflict of interest statement

No competing interests were disclosed.

References

  1. Virus Genes. 2013 Dec;47(3):569-73 - PubMed
  2. PLoS Med. 2016 Apr 12;13(4):e1002002 - PubMed
  3. J Appl Ecol. 2008 Aug;45(4):1246-1257 - PubMed
  4. Science. 2018 Jul 13;361(6398):130-131 - PubMed
  5. BMC Bioinformatics. 2018 Dec 18;19(1):532 - PubMed
  6. Infect Genet Evol. 2016 Mar;38:22-28 - PubMed
  7. Genome Biol. 2019 Jan 8;20(1):8 - PubMed
  8. PLoS Pathog. 2016 Apr 08;12(4):e1005525 - PubMed
  9. Emerg Infect Dis. 2017 Sep;23(9):1454-1461 - PubMed
  10. Parasitology. 2016 Jun;143(7):821-34 - PubMed
  11. Vet Rec. 2015 Feb 28;176(9):220-5 - PubMed
  12. Bioinformatics. 2009 Jul 15;25(14):1754-60 - PubMed
  13. Virus Evol. 2017 Dec 13;3(2):vex038 - PubMed
  14. Philos Trans R Soc Lond B Biol Sci. 2017 Jul 19;372(1725): - PubMed
  15. Genes (Basel). 2019 Aug 29;10(9): - PubMed
  16. Virus Res. 2005 Jul;111(1):13-27 - PubMed
  17. Emerg Infect Dis. 2019 Jan;25(1):82-91 - PubMed
  18. Lancet Glob Health. 2016 Nov;4(11):e780-e781 - PubMed
  19. Mol Biol Evol. 2013 Apr;30(4):772-80 - PubMed
  20. PLoS Pathog. 2016 Dec 15;12(12):e1006041 - PubMed
  21. Philos Trans R Soc Lond B Biol Sci. 2013 Jun 24;368(1623):20120137 - PubMed
  22. PLoS Negl Trop Dis. 2016 Oct 5;10(10):e0005010 - PubMed
  23. Antiviral Res. 2017 Jul;143:1-12 - PubMed
  24. Vaccine. 2011 Dec 30;29 Suppl 4:D7-9 - PubMed
  25. PLoS Negl Trop Dis. 2018 Sep 6;12(9):e0006367 - PubMed
  26. Bioinformatics. 2014 May 1;30(9):1312-3 - PubMed
  27. Science. 2018 Aug 31;361(6405):894-899 - PubMed
  28. Trends Microbiol. 2018 Dec;26(12):1035-1048 - PubMed
  29. BMC Genomics. 2013 Jul 04;14:444 - PubMed
  30. Science. 2017 Jul 14;357(6347):146-148 - PubMed
  31. Mol Ecol. 2018 Feb;27(3):773-788 - PubMed
  32. Genes (Basel). 2019 Aug 21;10(9): - PubMed
  33. Genome Biol. 2015 May 30;16:114 - PubMed
  34. J Surg Res. 2018 Mar;223:136-141 - PubMed
  35. Trends Parasitol. 2004 Aug;20(8):347-51 - PubMed
  36. Nature. 2017 Jun 15;546(7658):406-410 - PubMed
  37. Nature. 2017 Apr 20;544(7650):309-315 - PubMed
  38. Nat Protoc. 2017 Jun;12(6):1261-1276 - PubMed
  39. Genome Med. 2016 Sep 29;8(1):97 - PubMed
  40. Science. 2014 Sep 26;345(6204):1562-4 - PubMed
  41. Genome Announc. 2017 Jul 6;5(27): - PubMed
  42. One Health. 2019 Feb 08;7:100082 - PubMed
  43. Rev Sci Tech. 2019 May;38(1):213-224 - PubMed
  44. Genome Biol. 2014 Nov 07;15(11):515 - PubMed
  45. Curr Opin Virol. 2014 Oct;8:68-72 - PubMed
  46. J Biomol Tech. 2017 Apr;28(1):2-7 - PubMed
  47. PLoS Negl Trop Dis. 2013 Apr 04;7(4):e2144 - PubMed
  48. Virus Res. 2017 Mar 15;232:123-133 - PubMed
  49. Virus Evol. 2015 Sep 10;1(1):vev011 - PubMed
  50. Nature. 2016 Feb 11;530(7589):228-232 - PubMed
  51. PLoS Pathog. 2012;8(6):e1002786 - PubMed
  52. Zoonoses Public Health. 2019 Feb;66(1):47-59 - PubMed
  53. PLoS Negl Trop Dis. 2019 Aug 5;13(8):e0007564 - PubMed
  54. Front Microbiol. 2018 Sep 19;9:2225 - PubMed
  55. Proc Biol Sci. 2007 Sep 7;274(1622):2123-30 - PubMed
  56. Proc Biol Sci. 2014 Mar 11;281(1782):20133251 - PubMed
  57. Nat Methods. 2015 Aug;12(8):733-5 - PubMed
  58. J Vis Exp. 2019 Jul 10;(149): - PubMed
  59. Mol Biol Evol. 2017 Oct 1;34(10):2563-2571 - PubMed
  60. Trop Med Infect Dis. 2019 Feb 07;4(1): - PubMed
  61. Mol Ecol. 2019 Sep;28(18):4335-4350 - PubMed
  62. Nat Rev Genet. 2018 Jan;19(1):9-20 - PubMed
  63. Trends Microbiol. 2018 Oct;26(10):886-887 - PubMed
  64. Sci Transl Med. 2017 Dec 20;9(421): - PubMed
  65. Euro Surveill. 2018 Dec;23(50): - PubMed

Publication Types

Grant support