publication . Other literature type . Article . 2014

Enhanced methods for unbiased deep sequencing of Lassa and Ebola RNA viruses from clinical and biological samples.

S Humarr Kahn; Donald S. Grant; Christian B. Matranga; Aaron M. Berlin; Sarah M. Winnicki; Sarah M. Winnicki; Onikepe A. Folarin; Bruce W. Birren; Robert F. Garry; Matthew Stremlau; ...
Open Access
  • Published: 01 Jan 2014
  • Publisher: Springer Science and Business Media LLC
  • Country: United States
Abstract
We have developed a robust RNA sequencing method for generating complete de novo assemblies with intra-host variant calls of Lassa and Ebola virus genomes in clinical and biological samples. Our method uses targeted RNase H-based digestion to remove contaminating poly(rA) carrier and ribosomal RNA. This depletion step improves both the quality of data and quantity of informative reads in unbiased total RNA sequencing libraries. We have also developed a hybrid-selection protocol to further enrich the viral content of sequencing libraries. These protocols have enabled rapid deep sequencing of both Lassa and Ebola virus and are broadly applicable to other viral gen...
Subjects
Medical Subject Headings: viruses
free text keywords: Method, Genome, Virology, Biology, Deep sequencing, Genomics, RNA, Ribosomal RNA, Lassa fever, medicine.disease, medicine, RNase P, Ebola virus, medicine.disease_cause
Funded by
NIH| Host and Pathogen Evolution in Lassa Fever
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 1DP2OD006514-01
  • Funding stream: OFFICE OF THE DIRECTOR, NATIONAL INSTITUTES OF HEALTH
50 references, page 1 of 4

Frame, JD, Baldwin, JM, Gocke, DJ, Troup, JM. Lassa fever, a new virus disease of man from West Africa. I. Clinical description and pathological findings. Am J Trop Med Hyg. 1970; 19: 670-676 [OpenAIRE] [PubMed]

Pattyn, S, van der Groen, G, Courteille, G, Jacob, W, Piot, P. Isolation of Marburg-like virus from a case of haemorrhagic fever in Zaire. Lancet. 1977; 1: 573-574 [OpenAIRE] [PubMed] [DOI]

Johnson, KM, Lange, JV, Webb, PA, Murphy, FA. Isolation and partial characterisation of a new virus causing acute haemorrhagic fever in Zaire. Lancet. 1977; 1: 569-571 [PubMed] [DOI]

Bowen, ET, Lloyd, G, Harris, WJ, Platt, GS, Baskerville, A, Vella, EE. Viral haemorrhagic fever in southern Sudan and northern Zaire. Preliminary studies on the aetiological agent. Lancet. 1977; 1: 571-573 [PubMed] [DOI]

Paessler, S, Walker, DH. Pathogenesis of the viral hemorrhagic fevers. Annu Rev Pathol. 2013; 8: 411-440 [OpenAIRE] [PubMed] [DOI]

Gire, SK, Stremlau, M, Andersen, KG, Schaffner, SF, Bjornson, Z, Rubins, K, Hensley, L, McCormick, JB, Lander, ES, Garry, RF, Happi, C, Sabeti, PC. Epidemiology. Emerging disease or diagnosis?. Science. 2012; 338: 750-752 [OpenAIRE] [PubMed] [DOI]

7.CDC website for Ebola 2014 outbreak. [http://www.cdc.gov/vhf/ebola/outbreaks/guinea/]

Meyer, BJ, de la Torre, JC, Southern, PJ. Arenaviruses: genomic RNAs, transcription, and replication. Curr Top Microbiol Immunol. 2002; 262: 139-157 [OpenAIRE] [PubMed]

McCormick, JB, King, IJ, Webb, PA, Johnson, KM, O’Sullivan, R, Smith, ES, Trippel, S, Tong, TC. A case-control study of the clinical diagnosis and course of Lassa fever. J Infect Dis. 1987; 155: 445-455 [OpenAIRE] [PubMed] [DOI]

Demby, AH, Inapogui, A, Kargbo, K, Koninga, J, Kourouma, K, Kanu, J, Coulibaly, M, Wagoner, KD, Ksiazek, TG, Peters, CJ, Rollin, PE, Bausch, DG. Lassa fever in Guinea: II. Distribution and prevalence of Lassa virus infection in small mammals. Vector Borne Zoonotic Dis. 2001; 1: 283-297 [OpenAIRE] [PubMed] [DOI]

Lecompte, E, Fichet-Calvet, E, Daffis, S, Koulemou, K, Sylla, O, Kourouma, F, Dore, A, Soropogui, B, Aniskin, V, Allali, B, Kouassi Kan, S, Lalis, A, Koivogui, L, Günther, S, Denys, C, ter Meulen, J. Mastomys natalensis and Lassa fever, West Africa. Emerg Infect Dis. 2006; 12: 1971-1974 [OpenAIRE] [PubMed] [DOI]

Booth, TF, Rabb, MJ, Beniac, DR. How do filovirus filaments bend without breaking?. Trends Microbiol. 2013; 21: 583-593 [OpenAIRE] [PubMed] [DOI]

Muhlberger, E, Weik, M, Volchkov, VE, Klenk, HD, Becker, S. Comparison of the transcription and replication strategies of marburg virus and Ebola virus by using artificial replication systems. J Virol. 1999; 73: 2333-2342 [OpenAIRE] [PubMed]

Bowen, MD, Rollin, PE, Ksiazek, TG, Hustad, HL, Bausch, DG, Demby, AH, Bajani, MD, Peters, CJ, Nichol, ST. Genetic diversity among Lassa virus strains. J Virol. 2000; 74: 6992-7004 [OpenAIRE] [PubMed] [DOI]

Vieth, S, Drosten, C, Lenz, O, Vincent, M, Omilabu, S, Hass, M, Becker-Ziaja, B, ter Meulen, J, Nichol, ST, Schmitz, H, Gunther, S. RT-PCR assay for detection of Lassa virus and related Old World arenaviruses targeting the L gene. Trans R Soc Trop Med Hyg. 2007; 101: 1253-1264 [OpenAIRE] [PubMed] [DOI]

50 references, page 1 of 4
Abstract
We have developed a robust RNA sequencing method for generating complete de novo assemblies with intra-host variant calls of Lassa and Ebola virus genomes in clinical and biological samples. Our method uses targeted RNase H-based digestion to remove contaminating poly(rA) carrier and ribosomal RNA. This depletion step improves both the quality of data and quantity of informative reads in unbiased total RNA sequencing libraries. We have also developed a hybrid-selection protocol to further enrich the viral content of sequencing libraries. These protocols have enabled rapid deep sequencing of both Lassa and Ebola virus and are broadly applicable to other viral gen...
Subjects
Medical Subject Headings: viruses
free text keywords: Method, Genome, Virology, Biology, Deep sequencing, Genomics, RNA, Ribosomal RNA, Lassa fever, medicine.disease, medicine, RNase P, Ebola virus, medicine.disease_cause
Funded by
NIH| Host and Pathogen Evolution in Lassa Fever
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 1DP2OD006514-01
  • Funding stream: OFFICE OF THE DIRECTOR, NATIONAL INSTITUTES OF HEALTH
50 references, page 1 of 4

Frame, JD, Baldwin, JM, Gocke, DJ, Troup, JM. Lassa fever, a new virus disease of man from West Africa. I. Clinical description and pathological findings. Am J Trop Med Hyg. 1970; 19: 670-676 [OpenAIRE] [PubMed]

Pattyn, S, van der Groen, G, Courteille, G, Jacob, W, Piot, P. Isolation of Marburg-like virus from a case of haemorrhagic fever in Zaire. Lancet. 1977; 1: 573-574 [OpenAIRE] [PubMed] [DOI]

Johnson, KM, Lange, JV, Webb, PA, Murphy, FA. Isolation and partial characterisation of a new virus causing acute haemorrhagic fever in Zaire. Lancet. 1977; 1: 569-571 [PubMed] [DOI]

Bowen, ET, Lloyd, G, Harris, WJ, Platt, GS, Baskerville, A, Vella, EE. Viral haemorrhagic fever in southern Sudan and northern Zaire. Preliminary studies on the aetiological agent. Lancet. 1977; 1: 571-573 [PubMed] [DOI]

Paessler, S, Walker, DH. Pathogenesis of the viral hemorrhagic fevers. Annu Rev Pathol. 2013; 8: 411-440 [OpenAIRE] [PubMed] [DOI]

Gire, SK, Stremlau, M, Andersen, KG, Schaffner, SF, Bjornson, Z, Rubins, K, Hensley, L, McCormick, JB, Lander, ES, Garry, RF, Happi, C, Sabeti, PC. Epidemiology. Emerging disease or diagnosis?. Science. 2012; 338: 750-752 [OpenAIRE] [PubMed] [DOI]

7.CDC website for Ebola 2014 outbreak. [http://www.cdc.gov/vhf/ebola/outbreaks/guinea/]

Meyer, BJ, de la Torre, JC, Southern, PJ. Arenaviruses: genomic RNAs, transcription, and replication. Curr Top Microbiol Immunol. 2002; 262: 139-157 [OpenAIRE] [PubMed]

McCormick, JB, King, IJ, Webb, PA, Johnson, KM, O’Sullivan, R, Smith, ES, Trippel, S, Tong, TC. A case-control study of the clinical diagnosis and course of Lassa fever. J Infect Dis. 1987; 155: 445-455 [OpenAIRE] [PubMed] [DOI]

Demby, AH, Inapogui, A, Kargbo, K, Koninga, J, Kourouma, K, Kanu, J, Coulibaly, M, Wagoner, KD, Ksiazek, TG, Peters, CJ, Rollin, PE, Bausch, DG. Lassa fever in Guinea: II. Distribution and prevalence of Lassa virus infection in small mammals. Vector Borne Zoonotic Dis. 2001; 1: 283-297 [OpenAIRE] [PubMed] [DOI]

Lecompte, E, Fichet-Calvet, E, Daffis, S, Koulemou, K, Sylla, O, Kourouma, F, Dore, A, Soropogui, B, Aniskin, V, Allali, B, Kouassi Kan, S, Lalis, A, Koivogui, L, Günther, S, Denys, C, ter Meulen, J. Mastomys natalensis and Lassa fever, West Africa. Emerg Infect Dis. 2006; 12: 1971-1974 [OpenAIRE] [PubMed] [DOI]

Booth, TF, Rabb, MJ, Beniac, DR. How do filovirus filaments bend without breaking?. Trends Microbiol. 2013; 21: 583-593 [OpenAIRE] [PubMed] [DOI]

Muhlberger, E, Weik, M, Volchkov, VE, Klenk, HD, Becker, S. Comparison of the transcription and replication strategies of marburg virus and Ebola virus by using artificial replication systems. J Virol. 1999; 73: 2333-2342 [OpenAIRE] [PubMed]

Bowen, MD, Rollin, PE, Ksiazek, TG, Hustad, HL, Bausch, DG, Demby, AH, Bajani, MD, Peters, CJ, Nichol, ST. Genetic diversity among Lassa virus strains. J Virol. 2000; 74: 6992-7004 [OpenAIRE] [PubMed] [DOI]

Vieth, S, Drosten, C, Lenz, O, Vincent, M, Omilabu, S, Hass, M, Becker-Ziaja, B, ter Meulen, J, Nichol, ST, Schmitz, H, Gunther, S. RT-PCR assay for detection of Lassa virus and related Old World arenaviruses targeting the L gene. Trans R Soc Trop Med Hyg. 2007; 101: 1253-1264 [OpenAIRE] [PubMed] [DOI]

50 references, page 1 of 4
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