Metagenomic sequencing with spiked primer enrichment for viral diagnostics and genomic surveillance

Deng, Xianding; Achari, Asmeeta; Federman, Scot; Yu, Guixia; Somasekar, Sneha; Bártolo, Inês; Yagi, Shigeo; Mbala-Kingebeni, Placide; Kapetshi, Jimmy; Ahuka‐Mundeke, Steve; Muyembe‐Tamfum, Jean‐Jacques; Ahmed, Asim A.; Ganesh, Vijay; Tamhankar, Manasi; Patterson, Jean L.; Ndembi, Nicaise; Mbanya, Dora; Kaptué, Lazare; McArthur, Carole; Muñoz-Medina, José Esteban; González-Bonilla, César; López, Susana; Arevalo, Shaun; Miller, Steve; Stone, Mars; Busch, Michael P.; Hsieh, Kristina; Messenger, Sharon; Wadford, Debra A.; Rodgers, Mary A.; Cloherty, Gavin; Faria, Nuno Rodrigues; Thézé, Julien; Pybus, Oliver G.; Neto, Zoraima; Morais, Joana; Taveira, Nuno; Hackett, John; Chiu, Charles Y.

doi:10.1038/s41564-019-0637-9

Cited by 144 publications

(124 citation statements)

References 56 publications

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“…The extracted RNA described above was converted to cDNA using MSSPE method (Metagenomic Sequencing with Spiked Primer Enrichment) as previously described (15). The custom designed SARS-CoV-2 primers (13-nucleotide in length, IDT Technologies) were constructed using 30 early SARS-CoV-2 genome references in the National Instiutes of Health (NIH) GenBank database, and were subsequently added to the reverse transcription process (Table S1).…”

Section: Whole Genome Sequencing Of Sars-cov2mentioning

confidence: 99%

A Genomic Survey of SARS-CoV-2 Reveals Multiple Introductions into Northern California without a Predominant Lineage

Deng

Federman

et al. 2020

Preprint

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The COVID-19 pandemic caused by the novel coronavirus SARS-CoV-2 has spread globally, resulting in >300,000 reported cases worldwide as of March 21st, 2020. Here we investigate the genetic diversity and genomic epidemiology of SARS-CoV-2 in Northern California using samples from returning travelers, cruise ship passengers, and cases of community transmission with unclear infection sources. Virus genomes were sampled from 29 patients diagnosed with COVID-19 infection from Feb 3rd through Mar 15th. Phylogenetic analyses revealed at least 8 different SARS-CoV-2 lineages, suggesting multiple independent introductions of the virus into the state. Virus genomes from passengers on two consecutive excursions of the Grand Princess cruise ship clustered with those from an established epidemic in Washington State, including the WA1 genome representing the first reported case in the United States on January 19th. We also detected evidence for presumptive transmission of SARS-CoV-2 lineages from one community to another. These findings suggest that cryptic transmission of SARS-CoV-2 in Northern California to date is characterized by multiple transmission chains that originate via distinct introductions from international and interstate travel, rather than widespread community transmission of a single predominant lineage. Rapid testing and contact tracing, social distancing, and travel restrictions are measures that will help to slow SARS-CoV-2 spread in California and other regions of the USA.

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Section: Whole Genome Sequencing Of Sars-cov2mentioning

confidence: 99%

A Genomic Survey of SARS-CoV-2 Reveals Multiple Introductions into Northern California without a Predominant Lineage

Deng

Federman

et al. 2020

Preprint

Self Cite

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“…To overcome this barrier, our follow-up steps included a target enrichment of SARS-CoV-2 while keeping the comprehensiveness of our mNGS pipeline intact. 6 For an emerging threat, this strategy offers the flexibility to successfully recover the pathogen genome in question for subsequent phylogenetic analyses without compromising discovery. However, the other key factor in mNGS success is the accessibility to open-access, cloud-based metagenomics bioinformatics pipelines, such as IDseq which automates the process of separating host sequence characterizing the remaining non-host sequences.…”

Section: Discussionmentioning

confidence: 99%

Rapid metagenomic characterization of a case of imported COVID-19 in Cambodia

Manning¹,

Bohl²,

Lay³

et al. 2020

Preprint

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Rapid production and publication of pathogen genome sequences during emerging disease outbreaks provide crucial public health information. In resource-limited settings, especially near an outbreak epicenter, conventional deep sequencing or bioinformatics are often challenging. Here we successfully used metagenomic next generation sequencing on an iSeq100 Illumina platform paired with an open-source bioinformatics pipeline to quickly characterize Cambodia's first case of COVID-

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“…Usually, the scalability of a metabarcoding approach is limited by genus level; however, this limitation is compensated for by a significant cost reduction in comparison with metagenomics. Unfortunately, no such loci have been described for viruses, owing primarily to their genetic diversity; however, some attempts have been made at solving this issue with broad-range primer panels, created by computational methods [144,145] with promising results.…”

Section: Target Amplificationmentioning

confidence: 99%

Current Trends in Diagnostics of Viral Infections of Unknown Etiology

Kiselev

Matsvay

Абрамов

et al. 2020

Viruses

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Viruses are evolving at an alarming rate, spreading and inconspicuously adapting to cutting-edge therapies. Therefore, the search for rapid, informative and reliable diagnostic methods is becoming urgent as ever. Conventional clinical tests (PCR, serology, etc.) are being continually optimized, yet provide very limited data. Could high throughput sequencing (HTS) become the future gold standard in molecular diagnostics of viral infections? Compared to conventional clinical tests, HTS is universal and more precise at profiling pathogens. Nevertheless, it has not yet been widely accepted as a diagnostic tool, owing primarily to its high cost and the complexity of sample preparation and data analysis. Those obstacles must be tackled to integrate HTS into daily clinical practice. For this, three objectives are to be achieved: (1) designing and assessing universal protocols for library preparation, (2) assembling purpose-specific pipelines, and (3) building computational infrastructure to suit the needs and financial abilities of modern healthcare centers. Data harvested with HTS could not only augment diagnostics and help to choose the correct therapy, but also facilitate research in epidemiology, genetics and virology. This information, in turn, could significantly aid clinicians in battling viral infections.

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Metagenomic sequencing with spiked primer enrichment for viral diagnostics and genomic surveillance

Cited by 144 publications

References 56 publications

A Genomic Survey of SARS-CoV-2 Reveals Multiple Introductions into Northern California without a Predominant Lineage

A Genomic Survey of SARS-CoV-2 Reveals Multiple Introductions into Northern California without a Predominant Lineage

Rapid metagenomic characterization of a case of imported COVID-19 in Cambodia

Current Trends in Diagnostics of Viral Infections of Unknown Etiology

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