Academic Journal
Targeted genomic sequencing with probe capture for discovery and surveillance of coronaviruses in bats
| العنوان: | Targeted genomic sequencing with probe capture for discovery and surveillance of coronaviruses in bats |
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| المؤلفون: | Kuchinski, Kevin S, Loos, Kara D, Suchan, Danae M, Russell, Jennifer N, Sies, Ashton N, Kumakamba, Charles, Muyembe, Francisca, Mbala Kingebeni, Placide, Ngay Lukusa, Ipos, N’Kawa, Frida, Atibu Losoma, Joseph, Makuwa, Maria, Gillis, Amethyst, LeBreton, Matthew, Ayukekbong, James A, Lerminiaux, Nicole A, Monagin, Corina, Joly, Damien O, Saylors, Karen, Wolfe, Nathan D, Rubin, Edward M, Muyembe Tamfum, Jean J, Prystajecky, Natalie A, McIver, David J, Lange, Christian E, Cameron, Andrew DS |
| المساهمون: | Genome Canada, Saskatchewan Health Research Foundation, United States Agency for International Development |
| المصدر: | eLife ; volume 11 ; ISSN 2050-084X |
| بيانات النشر: | eLife Sciences Publications, Ltd |
| سنة النشر: | 2022 |
| المجموعة: | eLife (E-Journal - via CrossRef) |
| الوصف: | Public health emergencies like SARS, MERS, and COVID-19 have prioritized surveillance of zoonotic coronaviruses, resulting in extensive genomic characterization of coronavirus diversity in bats. Sequencing viral genomes directly from animal specimens remains a laboratory challenge, however, and most bat coronaviruses have been characterized solely by PCR amplification of small regions from the best-conserved gene. This has resulted in limited phylogenetic resolution and left viral genetic factors relevant to threat assessment undescribed. In this study, we evaluated whether a technique called hybridization probe capture can achieve more extensive genome recovery from surveillance specimens. Using a custom panel of 20,000 probes, we captured and sequenced coronavirus genomic material in 21 swab specimens collected from bats in the Democratic Republic of the Congo. For 15 of these specimens, probe capture recovered more genome sequence than had been previously generated with standard amplicon sequencing protocols, providing a median 6.1-fold improvement (ranging up to 69.1-fold). Probe capture data also identified five novel alpha- and betacoronaviruses in these specimens, and their full genomes were recovered with additional deep sequencing. Based on these experiences, we discuss how probe capture could be effectively operationalized alongside other sequencing technologies for high-throughput, genomics-based discovery and surveillance of bat coronaviruses. |
| نوع الوثيقة: | article in journal/newspaper |
| اللغة: | English |
| DOI: | 10.7554/elife.79777 |
| الاتاحة: | http://dx.doi.org/10.7554/elife.79777 https://cdn.elifesciences.org/articles/79777/elife-79777-v1.pdf https://cdn.elifesciences.org/articles/79777/elife-79777-v1.xml https://elifesciences.org/articles/79777 |
| Rights: | http://creativecommons.org/licenses/by/4.0/ ; http://creativecommons.org/licenses/by/4.0/ ; http://creativecommons.org/licenses/by/4.0/ |
| رقم الانضمام: | edsbas.DBEC8FD5 |
| قاعدة البيانات: | BASE |
| DOI: | 10.7554/elife.79777 |
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