Targeted genomic sequencing with probe capture for discovery and surveillance of coronaviruses in bats.
Kevin S KuchinskiKara D LoosDanae M SuchanJennifer N RussellAshton N SiesCharles KumakambaFrancisca MuyembePlacide Mbala KingebeniIpos Ngay LukusaFrida N'KawaJoseph Atibu LosomaMaria MakuwaAmethyst GillisMatthew LeBretonJames A AyukekbongNicole A LerminiauxCorina MonaginDamien O JolyKaren SaylorsNathan D WolfeEdward M RubinJean J Muyembe TamfumNatalie A PrystajeckyDavid J McIverChristian E LangeAndrew D S CameronPublished in: eLife (2022)
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 <i>alpha-</i> and <i>betacoronaviruses</i> 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.
Keyphrases
- sars cov
- public health
- single cell
- living cells
- high throughput
- respiratory syndrome coronavirus
- copy number
- quantum dots
- genome wide
- small molecule
- single molecule
- fluorescent probe
- fine needle aspiration
- electronic health record
- global health
- transcription factor
- photodynamic therapy
- gene expression
- big data
- drug delivery
- genome wide identification