Rapid viral metagenomics using SMART-9N amplification and nanopore sequencing

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Citações na Scopus
5
Tipo de produção
article
Data de publicação
2023
DOI
Scopus
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Título do Volume
Editora
F1000 RESEARCH LTD
Autores
PAULA, A. de
Citação
WELLCOME OPEN RESEARCH, v.6, article ID 241, p, 2023
Projetos de Pesquisa
Unidades Organizacionais
Fascículo
Resumo
Emerging and re-emerging viruses are a global health concern. Genome sequencing as an approach for monitoring circulating viruses is currently hampered by complex and expensive methods. Untargeted, metagenomic nanopore sequencing can provide genomic information to identify pathogens, prepare for or even prevent outbreaks. SMART (Switching Mechanism at the 5′ end of RNA Template) is a popular approach for RNA-Seq but most current methods rely on oligo-dT priming to target polyadenylated mRNA molecules. We have developed two random primed SMART-Seq approaches, a sequencing agnostic approach ‘SMART-9N’ and a version compatible rapid adapters  available from Oxford Nanopore Technologies ‘Rapid SMART-9N’. The methods were developed using viral isolates, clinical samples, and compared to a gold-standard amplicon-based method. From a Zika virus isolate the SMART-9N approach recovered 10kb of the 10.8kb RNA genome in a single nanopore read. We also obtained full genome coverage at a high depth coverage using the Rapid SMART-9N, which takes only 10 minutes and costs up to 45% less than other methods. We found the limits of detection of these methods to be 6 focus forming units (FFU)/mL with 99.02% and 87.58% genome coverage for SMART-9N and Rapid SMART-9N respectively. Yellow fever virus plasma samples and SARS-CoV-2 nasopharyngeal samples previously confirmed by RT-qPCR with a broad range of Ct-values were selected for validation. Both methods produced greater genome coverage when compared to the multiplex PCR approach and we obtained the longest single read of this study (18.5 kb) with a SARS-CoV-2 clinical sample, 60% of the virus genome using the Rapid SMART-9N method. This work demonstrates that SMART-9N and Rapid SMART-9N are sensitive, low input, and long-read compatible alternatives for RNA virus detection and genome sequencing and Rapid SMART-9N improves the cost, time, and complexity of laboratory work.
Palavras-chave
diagnostic, genomic surveillance, metagenomic, nanopore sequencing, RNA virus, SARS-CoV-2, YFV, ZIKV
URI
https://observatorio.fm.usp.br/handle/OPI/58600
Referências
  1. Devaux C.A., Emerging and re-emerging viruses: A global challenge illustrated by Chikungunya virus outbreaks, World J Virol, 1, 1, pp. 11-22, (2012)
  2. Miller S., Naccache S.N., Samayoa E., Et al., Laboratory validation of a clinical metagenomic sequencing assay for pathogen detection in cerebrospinal fluid, Genome Res, 29, 5, pp. 831-842, (2019)
  3. Washington J.A., Principles of Diagnosis, (1996)
  4. Wilson M.R., Naccache S.N., Samayoa E., Et al., Actionable diagnosis of neuroleptospirosis by next-generation sequencing, N Engl J Med, 370, 25, pp. 2408-2417, (2014)
  5. Quick J., Loman N.J., Duraffour S., Et al., Real-time, portable genome sequencing for Ebola surveillance, Nature, 530, 7589, pp. 228-232, (2016)
  6. Faria N.R., Quick J., Claro I.M., Et al., Establishment and cryptic transmission of Zika virus in Brazil and the Americas, Nature, 546, 7658, pp. 406-410, (2017)
  7. Naveca F.G., Claro I., Giovanetti M., Et al., Genomic, epidemiological and digital surveillance of Chikungunya virus in the Brazilian Amazon, PLoS Negl Trop Dis, 13, 3, (2019)
  8. de Jesus J.G., Dutra K.R., Sales F.C.D.S., Et al., Genomic detection of a virus lineage replacement event of dengue virus serotype 2 in Brazil, 2019, Mem Inst Oswaldo Cruz, 115, (2020)
  9. Faria N.R., Kraemer M.U.G., Hill S.C., Et al., Genomic and epidemiological monitoring of yellow fever virus transmission potential, Science, 361, 6405, pp. 894-899, (2018)
  10. Houldcroft C.J., Beale M.A., Breuer J., Clinical and biological insights from viral genome sequencing, Nat Rev Microbiol, 15, 3, pp. 183-192, (2017)
  11. Palacios G., Druce J., Du L., Et al., A new arenavirus in a cluster of fatal transplant-associated diseases, N Engl J Med, 358, 10, pp. 991-998, (2008)
  12. Nakamura S., Yang C.S., Sakon N., Et al., Direct metagenomic detection of viral pathogens in nasal and fecal specimens using an unbiased high-throughput sequencing approach, PLoS One, 4, 1, (2009)
  13. Manso C.F., Bibby D.F., Mbisa J.L., Efficient and unbiased metagenomic recovery of RNA virus genomes from human plasma samples, Sci Rep, 7, 1, (2017)
  14. Gu W., Miller S., Chiu C.Y., Clinical Metagenomic Next-Generation Sequencing for Pathogen Detection, Annu Rev Pathol, 14, pp. 319-338, (2019)
  15. Frey K.G., Herrera-Galeano J.E., Redden C.L., Et al., Comparison of three next-generation sequencing platforms for metagenomic sequencing and identification of pathogens in blood, BMC Genomics, 15, (2014)
  16. Kafetzopoulou L.E., Efthymiadis K., Lewandowski K., Et al., Assessment of metagenomic Nanopore and Illumina sequencing for recovering whole genome sequences of chikungunya and dengue viruses directly from clinical samples, Euro Surveill, 23, 50, (2018)
  17. Lewandowski K., Xu Y., Pullan S.T., Et al., Metagenomic Nanopore Sequencing of Influenza Virus Direct from Clinical Respiratory Samples, J Clin Microbiol, 58, 1, pp. e00963-e919, (2019)
  18. Reyes G.R., Kim J.P., Sequence-independent, single-primer amplification (SISPA) of complex DNA populations, Mol Cell Probes, 5, 6, pp. 473-481, (1991)
  19. Zhu Y.Y., Machleder E.M., Chenchik A., Et al., Reverse transcriptase template switching: a SMART approach for full-length cDNA library construction, Biotechniques, 30, 4, pp. 892-897, (2001)
  20. Quick J., Grubaugh N.D., Pullan S.T., Et al., Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples, Nat Protoc, 12, 6, pp. 1261-1276, (2017)
  21. Lanciotti R.S., Kosoy O.L., Laven J.J., Et al., Genetic and serologic properties of Zika virus associated with an epidemic, Yap State, Micronesia, 2007, Emerg Infect Dis, 14, 8, pp. 1232-1239, (2008)
  22. Silva-Filho J.L., de Oliveira L.G., Monteiro L., Et al., Gas6 drives Zika virus-induced neurological complications in humans and congenital syndrome in immunocompetent mice, Brain Behav Immun, 97, pp. 260-274, (2021)
  23. Fischer C., Torres M.C., Patel P., Et al., Lineage-Specific Real-Time RT-PCR for Yellow Fever Virus Outbreak Surveillance, Brazil, Emerg Infect Dis, 23, 11, pp. 1867-1871, (2017)
  24. Corman V.M., Landt O., Kaiser M., Et al., Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR, Euro Surveill, 25, 3, (2020)
  25. Tyson J.R., James P., Stoddart D., Et al., Improvements to the ARTIC multiplex PCR method for SARS-CoV-2 genome sequencing using nanopore, bioRxiv, (2020)
  26. Li H., Minimap2: pairwise alignment for nucleotide sequences, Bioinformatics, 34, 18, pp. 3094-3100, (2018)
  27. Li H., Handsaker B., Wysoker A., Et al., The Sequence Alignment/Map format and SAMtools, Bioinformatics, 25, 16, pp. 2078-2079, (2009)
  28. De Coster W., D'Hert S., Schultz D.T., Et al., NanoPack: visualizing and processing long-read sequencing data, Bioinformatics, 34, 15, pp. 2666-2669, (2018)
  29. Milne I., Bayer M., Cardle L., Et al., Tablet--next generation sequence assembly visualization, Bioinformatics, 26, 3, pp. 401-402, (2010)
  30. Kallas E.G., D'Elia Zanella L.G.F.A.B., Moreira C.H.V., Et al., Predictors of mortality in patients with yellow fever: an observational cohort study, Lancet Infect Dis, 19, 7, pp. 750-758, (2019)
  31. Gire S.K., Goba A., Andersen K.G., Et al., Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak, Science, 345, 6202, pp. 1369-1372, (2014)
  32. Salipante S.J., SenGupta D.J., Cummings L.A., Et al., Application of whole-genome sequencing for bacterial strain typing in molecular epidemiology, J Clin Microbiol, 53, 4, pp. 1072-1079, (2015)
  33. Deurenberg R.H., Bathoorn E., Chlebowicz M.A., Et al., Application of next generation sequencing in clinical microbiology and infection prevention, J Biotechnol, 243, pp. 16-24, (2017)
  34. Carbo E.C., Sidorov I.A., Zevenhoven-Dobbe J.C., Et al., Coronavirus discovery by metagenomic sequencing: a tool for pandemic preparedness, J Clin Virol, 131, (2020)
  35. Zhou P., Yang X.L., Wang X.G., Et al., A pneumonia outbreak associated with a new coronavirus of probable bat origin, Nature, 579, 7798, pp. 270-273, (2020)
  36. Nawy T., Single-cell sequencing, Nat Methods, 11, 1, (2014)
  37. Eberwine J., Sul J.Y., Bartfai T., Et al., The promise of single-cell sequencing, Nat Methods, 11, 1, pp. 25-27, (2014)
  38. Stephens Z., Wang C., Iyer R.K., Et al., Detection and visualization of complex structural variants from long reads, BMC Bioinformatics, 19, (2018)
  39. Fuselli S., Baptista R.P., Panziera A., Et al., A new hybrid approach for MHC genotyping: high-throughput NGS and long read MinION nanopore sequencing, with application to the non-model vertebrate Alpine chamois (Rupicapra rupicapra), Heredity (Edinb), 121, 4, pp. 293-303, (2018)

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