Wildy Prize Lecture, 2020–2021: Who wouldn’t want to discover a new virus?

Abstract

Innovations in science education are desperately needed to find ways to engage and interest students early in their undergraduate careers. Exposing students to authentic research experiences is highly beneficial, but finding ways to include all types of students and to do this at large scale is especially challenging. An attractive solution is the concept of an inclusive research education community (iREC) in which centralized research leadership and administration supports multiple institutions, including diverse groups of schools and universities, faculty and students. The Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Sciences (SEA-PHAGES) programme is an excellent example of an iREC, in which students explore viral diversity and evolution through discovery and genomic analysis of novel bacteriophages. The SEA-PHAGES programme has proven to be sustainable, to be implemented at large scale, and to enhance student persistence in science, as well as to produce substantial research advances. Discovering a new virus with the potential for new biological insights and clinical applications is inherently exciting. Who wouldn’t want to discover a new virus?

Mycobacteriophages: From Petri dish to patient

“…An alternative approach—metagenomic analysis of enriched viral samples—is also attractive, but generally provides informative data sets rather than individual phages that can be propagated, engineered, investigated mechanistically, and potentially used translationally. Envisaging the need to isolate phages at substantial scale, we developed integrated research-education programs in which phage discovery and genomics is the primary goal, providing research opportunities to young scientists including high school students and first year undergraduate students [ 25 ]. The Phage Hunters Integrating Research and Education (PHIRE) starting in 2002 provided research experiences locally in Pittsburgh [ 26 , 27 ] with the platform expanding into the Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) in 2008 [ 28 , 29 ]; both programs are supported by the Howard Hughes Medical Institute (HHMI).…”

PhaMMseqs: a new pipeline for constructing phage gene phamilies using MMseqs2

“…Pham assembly is broadly useful for phage comparative genomics, and central to phage database resources used in integrated research-education programs such as PHIRE and SEA-PHAGES ( Jordan et al 2014 ; Hanauer et al 2017 ; Hatfull 2021 ). With rapid increases in the number of genomes available for analysis, rapid sequence comparison algorithms are needed, and we demonstrate here that MMseqs2 can be effectively used for pham assembly, both in terms of computational speed and capacity as well as the overall quality of assembled phams.…”

Complete Genome Sequences of Cluster A Mycobacteriophages Kenmech and Peterson and Cluster F Mycobacteriophage Rockne

“… Mycobacterium smegmatis has served as a model organism for studying pathogenic Mycobacteria . Recently, bacteriophages isolated on Mycobacterium smegmatis have been used as a therapeutic to treat mycobacterial infections ( 1 – 3 ). The isolation and characterization of novel mycobacteriophages can therefore serve to increase our understanding of their genetic diversity as well as the repertoire of candidate phages for therapeutic use.…”