Archaeal viruses, not archaeal phages: an archaeological dig

Abstract

Viruses infect members of domains Bacteria, Eukarya, and Archaea. While those infecting domain Eukarya are nearly universally described as "Viruses", those of domain Bacteria, to a substantial extent, instead are called "Bacteriophages," or "Phages." Should the viruses of domain Archaea therefore be dubbed "Archaeal phages," "Archaeal viruses," or some other construct? Here we provide documentation of published, general descriptors of the viruses of domain Archaea. Though at first the term "Phage" or equivalent was used almost exclusively in the archaeal virus literature, there has been a nearly 30-year trend away from this usage, with some persistence of "Phage" to describe "Head-and-tail" archaeal viruses, "Halophage" to describe viruses of halophilic Archaea, use of "Prophage" rather than "Provirus," and so forth. We speculate on the root of the early 1980's transition from "Phage" to "Virus" to describe these infectious agents, consider the timing of introduction of "Archaeal virus" (which can be viewed as analogous to "Bacterial virus"), identify numerous proposed alternatives to "Archaeal virus," and also provide discussion of the general merits of the term, "Phage." Altogether we identify in excess of one dozen variations on how the viruses of domain Archaea are described, and document the timing of both their introduction and use.

Figure 1

Various names that have been used to generally describe archaeal viruses as well as subsets of those viruses (e.g., “Halophage”). A sampling of those terms along with what to the best of our knowledge are their dates of introduction into the literature are presented in a timeline format. Note in particular the diversity as well as, even over the last decade, an apparently ongoing lack of consensus. References for first use, again to the best of our knowledge, are as follows: Bacteriophage (and Phage) [11], Halophage [12], Archaebacterial phage [13], Virus [13] (see, however, also [14]), Archaebacterial virus [15], Archaebacteriophage [16], Archaeobacteriophage [17], Archaeal phage [18], Archaeophage [19], Archaeal virus [20], Archaebacterial bacteriophage [21], Archaea virus [22], Archaevirus [23], Archaephage [24], Archaeavirus [25], Archael virus [26] (also found as a typo in a 1999 publication [27]), Archeal virus [28], Archeophage [29], Archaeovirus [30, 31], Archeovirus [32], Archaeon virus [33], Archae virus [34], and Archaean virus [35].

Figure 2

Counting publications using “Virus” (green hexagons), “Phage” (blue circles), “Halophage” (black squares), “Prophage” (“hourglass” circles), and an aggregate of all three phage terms, “All phage” (red Xs) to describe archaeal viruses. Presented are (a) the absolute number of publications, (b) the relative number of “All phage” versus “Virus”, (c) just “All phage”, and (d) just “Virus” (with (c) and (d) provided solely for clarity rather than to provide additional information). Shown are numbers of “Yes” statuses as indicated in Table 1, supplementary materials, but not “Yes/No” nor “No” entries.