Genomic and virologic characterization of samples from a shipboard outbreak of COVID-19 reveals distinct variants within limited temporospatial parameters

Next-Generation Sequencing and Bioinformatics Consortium Approach to Genomic Surveillance

Genomic surveillance programs benefit greatly from a network of committed, well-supported laboratories that conduct ongoing surveillance activities for pathogens of public health importance. The experiences of the Global Emerging Infections Surveillance program provide insights for building and maintaining genomic surveillance capabilities for public health and pandemic preparedness and response. To meet the needs of US Department of Defense and the Military Health System to use genomics to monitor pathogens of military and public health importance, Global Emerging Infections Surveillance convened a consortium of experts in genome sequencing, bioinformatics, and genomic epidemiology. The experts developed a 3-tiered framework for building and maintaining next-generation sequencing and bioinformatics capabilities for genomic surveillance within the Department of Defense. The consortium strategy was developed before the COVID-19 pandemic, leading to a network prepared to respond with existing resources and expand as new funding became available.

A proof of concept for a targeted enrichment approach to the simultaneous detection and characterization of rickettsial pathogens from clinical specimens

Infection with either Rickettsia prowazekii or Orientia tsutsugamushi is common, yet diagnostic capabilities are limited due to the short window for positive identification. Until now, although targeted enrichment had been applied to increase sensitivity of sequencing-based detection for various microorganisms, it had not been applied to sequencing of R. prowazekii in clinical samples. Additionally, hybridization-based targeted enrichment strategies had only scarcely been applied to qPCR of any pathogens in clinical samples. Therefore, we tested a targeted enrichment technique as a proof of concept and found that it dramatically reduced the limits of detection of these organisms by both qPCR and high throughput sequencing. The enrichment methodology was first tested in contrived clinical samples with known spiked-in concentrations of R. prowazekii and O. tsutsugamushi DNA. This method was also evaluated using clinical samples, resulting in the simultaneous identification and characterization of O. tsutsugamushi directly from clinical specimens taken from sepsis patients. We demonstrated that the targeted enrichment technique is helpful by lowering the limit of detection, not only when applied to sequencing, but also when applied to qPCR, suggesting the technique could be applied more broadly to include other assays and/or microbes for which there are limited diagnostic or detection modalities.