التفاصيل البيبلوغرافية
| العنوان: |
Development of an amplicon-based sequencing approach in response to the global emergence of mpox |
| المؤلفون: |
Chen, Nicholas F. G., Chaguza, Chrispin, Gagne, Luc, Doucette, Matthew, Smole, Sandra, Buzby, Erika, Hall, Joshua, Ash, Stephanie, Harrington, Rachel, Cofsky, Seana, Clancy, Selina, Kapsak, Curtis J., Sevinsky, Joel, Libuit, Kevin, Park, Daniel J., Hemarajata, Peera, Garrigues, Jacob M., Green, Nicole M., Sierra-Patev, Sean, Carpenter-Azevedo, Kristin, Huard, Richard C., Pearson, Claire, Incekara, Kutluhan, Nishimura, Christina, Huang, Jian Ping, Gagnon, Emily, Reever, Ethan, Razeq, Jafar, Muyombwe, Anthony, Borges, Vítor, Ferreira, Rita, Sobral, Daniel, Duarte, Silvia, Santos, Daniela, Vieira, Luís, Gomes, João Paulo, Aquino, Carly, Savino, Isabella M., Felton, Karinda, Bajwa, Moneeb, Hayward, Nyjil, Miller, Holly, Naumann, Allison, Allman, Ria, Greer, Neel, Fall, Amary, Mostafa, Heba H., McHugh, Martin P., Maloney, Daniel M., Dewar, Rebecca |
| المساهمون: |
Sugden, Bill, National Center for Advancing Translational Sciences, European Center for Disease Control |
| المصدر: |
PLOS Biology ; volume 21, issue 6, page e3002151 ; ISSN 1545-7885 |
| بيانات النشر: |
Public Library of Science (PLoS) |
| سنة النشر: |
2023 |
| المجموعة: |
PLOS Publications (via CrossRef) |
| الوصف: |
The 2022 multicountry mpox outbreak concurrent with the ongoing Coronavirus Disease 2019 (COVID-19) pandemic further highlighted the need for genomic surveillance and rapid pathogen whole-genome sequencing. While metagenomic sequencing approaches have been used to sequence many of the early mpox infections, these methods are resource intensive and require samples with high viral DNA concentrations. Given the atypical clinical presentation of cases associated with the outbreak and uncertainty regarding viral load across both the course of infection and anatomical body sites, there was an urgent need for a more sensitive and broadly applicable sequencing approach. Highly multiplexed amplicon-based sequencing (PrimalSeq) was initially developed for sequencing of Zika virus, and later adapted as the main sequencing approach for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Here, we used PrimalScheme to develop a primer scheme for human monkeypox virus that can be used with many sequencing and bioinformatics pipelines implemented in public health laboratories during the COVID-19 pandemic. We sequenced clinical specimens that tested presumptively positive for human monkeypox virus with amplicon-based and metagenomic sequencing approaches. We found notably higher genome coverage across the virus genome, with minimal amplicon drop-outs, in using the amplicon-based sequencing approach, particularly in higher PCR cycle threshold (Ct) (lower DNA titer) samples. Further testing demonstrated that Ct value correlated with the number of sequencing reads and influenced the percent genome coverage. To maximize genome coverage when resources are limited, we recommend selecting samples with a PCR Ct below 31 Ct and generating 1 million sequencing reads per sample. To support national and international public health genomic surveillance efforts, we sent out primer pool aliquots to 10 laboratories across the United States, United Kingdom, Brazil, and Portugal. These public health laboratories successfully implemented ... |
| نوع الوثيقة: |
article in journal/newspaper |
| اللغة: |
English |
| DOI: |
10.1371/journal.pbio.3002151 |
| الإتاحة: |
https://doi.org/10.1371/journal.pbio.3002151Test |
| حقوق: |
http://creativecommons.org/licenses/by/4.0Test/ |
| رقم الانضمام: |
edsbas.6E2DB736 |
| قاعدة البيانات: |
BASE |
